In situ hybridization detection method

ABSTRACT

The invention provides compositions and methods for the detection of targets in a sample; in particular, an in situ hybridization (ISH) sample. Probes and detectable labels may be provided in multiple layers in order to increase the flexibility of a detection system, and to allow for amplification to enhance the signal from a target. The layers may be created by incorporating probes and detectable labels into larger molecular units that interact through nucleic acids base-pairing, including peptide-nucleic acid (PNA) base-pairing. Optional non-natural bases allow for degenerate base pairing schemes. The compositions and methods are also compatible with immunohistochemistry (IHC), immunocytochemistry (ICC), flow cytometry, enzyme immuno-assays (EIA), enzyme linked immuno-assays (ELISA), blotting methods (e.g. Western, Southern, and Northern), labeling inside electrophoresis systems or on surfaces or arrays, and precipitation, among other general detection assay formats. The invention is also compatible with many different types of targets, probes, and detectable labels.

RELATED APPLICATIONS

This application is a continuation of U.S. application Ser. No.11/993,571, filed on Dec. 21, 2007, now U.S. Pat. No. 9,017,992, whichwas a national stage filing under 35 U.S.C. 371 of InternationalApplication No. PCT/IB2006/003123 filed on Jun. 30, 2006, whichinternational application claims priority to three U.S. ProvisionalPatent Application Nos.: 60/695,408; 60/695,409; and 60/695,410; each ofwhich was filed on Jul. 1, 2005. All of those applications areincorporated herein by reference.

BACKGROUND AND SUMMARY OF THE INVENTION

The invention provides compositions and methods for the detection oftargets in a sample, including an in situ hybridization (ISH) sample.Probes and detectable labels may be provided in multiple layers in orderto increase the flexibility of a detection system, and to enhance thesignal from a target. The compositions and methods are compatible with avariety of detection systems, and with many different types of targets,probes, and detectable labels.

Detection of a target in a sample may ordinarily be achieved bycontacting the target with a probe that specifically recognizes it. Theprobe may be linked, either directly or indirectly to a detectablelabel, such as a fluorophore or radioactive tag, which provides a signalrepresenting the target.

Some detection systems also provide ways of enhancing the signal fromthe target. For example, the label's signal may be enhanced byincreasing the number of detectable labels used to detect each target,or by instrumentation that may amplify the signal. Alternatively, if thetarget is an antigen, a multiple-antibody system may amplify thedetection signal. For instance, the target may first be bound by aprimary antibody, which, in turn, is capable of binding many secondaryantibodies or even tertiary antibodies, which, in their turn, bind tothe probe. This method, thus, increases the number of probes thatrecognize each antigen target by adding extra layers of molecularinteractions between the probe and target.

The secondary antibody technique is widely used, but may be limited dueto, for example i) the availability of the secondary antibodies; ii)unwanted cross reactivity between closely related species, e.g. rat,mouse; iii) the size of antibodies reduces the penetration of thereagents. Furthermore, conjugation of antibodies to other antibodies,enzymes, color labels, etc. is somewhat unique for every antibody due tobiological variations. Fab or Fab2 fragments of IgG have been used toovercome the size and non-specific binding problems, but such secondaryantibody based visualization systems still remain limited to staining ofone, two or three different targets. Amplification of the signal fromindividual targets is both laborious and complex due to theabove-mentioned technical limitations. Further, currently usedantibody-based amplification methods may only be of practical use withcertain types of targets and detectable labels. In contrast, the instantinvention uses the flexibility of nucleic acid hybridization to providea general set of compositions and methods that may be used to detect oneor many targets in a sample and amplify their signals.

The instant methods and compositions may also provide for increasedflexibility as compared to, for example, capture assays or sandwichassays, such as those described in U.S. Pat. No. 4,868,105, for example,that rely on one type of binding interaction such as a hapten-protein orprimary antibody-secondary antibody interaction. The ability to design avariety of nucleic acid analog hybridization pairs, for instance, maydramatically increase the ways in which the probe and detectable labelmay interact.

In some embodiments of the invention, compositions and methods mayseparate the probe and the detectable label such that they may becomprised on different units within a detection system. See, forexample, FIGS. 1a and 1c . The units may then interact through specifichybridization of nucleic acid analog segments. The units may be designedsuch that a given probe may interact with a variety of differentdetectable labels, depending upon the needs of the assay. The units mayalso be designed to include multiple interacting nucleic acid analogsegments, either to increase the affinity between the units, or toamplify a signal. Further, adaptor units may be included that provide,for example, one or more additional molecular layers between the probeand the detectable label. See FIG. 1b . In some embodiments, the adaptorunits may allow for even greater mixing and matching of probes andlabels as well as additional amplification of a signal. The componentsof the instant compositions may also be designed to be of similarchemical compositions so that they may be prepared simply usingstandardized conjugation schemes.

Due to the relative ease with which nucleic acid hybridization schemesmay be planned, the methods and compositions of the invention may alsobe used to detect more than one target within a sample. For instance,multiple targets in a sample are not always expressed in equal amounts.Thus, there may be a differential need for amplification. The instantinvention is also useful in normalizing the detection of two or moretargets in a system.

The system may also be designed such that one unit specificallyhybridizes to more than one other unit. For instance, the various unitsof the invention may be designed such that one unit hybridizes toseveral other units, for example, by providing multiple nucleic acidanalog segments on the same unit. Alternatively, certain nucleic acidanalogs may allow for degenerate hybridization schemes such that onenucleic acid analog segment may specifically hybridize to more than oneother nucleic acid analog segment, creating a “master key” unit. (Seethe international application entitled “New Nucleic Acid Base Pairs”submitted herewith, for an example of such segments.) This uniquefeature increases the flexibility of the instant compositions andmethods even further.

Moreover, the instant compositions and methods are compatible with alarge variety of samples and are adaptable to a large number of targets,probes, and detectable labels. The present invention is useful in insitu hybridization (ISH), but can be applied to other detection methodsas well, such as immunohistochemistry (IHC), immunocytochemistry (ICC),flow cytometry, enzyme immuno-assays (EIA), enzyme linked immuno-assays(ELISA), blotting methods (e.g. Western, Southern, and Northern),labeling inside electrophoresis systems or on surfaces or arrays, andprecipitation, among others. Such detection formats, for example, areuseful in research as well as in diagnosing diseases or conditions.Further, if multiple targets are detected, such systems may be useful inanalyzing expression patterns of genes or levels of proteins within asample.

It is to be understood that both the foregoing general description andthe following detailed description are exemplary and explanatory onlyand are not restrictive of the invention, as claimed. Additional objectsand advantages of the invention will be set forth in part in thedescription which follows, and in part will be obvious from thedescription, or may be learned by practice of the invention.

BRIEF DESCRIPTION OF THE DRAWINGS

The accompanying drawings, which are incorporated in and constitute apart of this specification, illustrate one several non-limitingembodiments of the invention.

FIG. 1a illustrates an exemplary recognition unit according to theinvention, comprising a nucleic acid analog segment (shaded bar), alinker (thin line), a polymer (thick line), and an antibody probe(upside-down Y shape).

FIG. 1b illustrates an exemplary optional adaptor unit according to theinvention, comprising two nucleic acid analog segments (shaded bars),linkers (thin lines), and a polymer (thick line).

FIG. 1c illustrates an exemplary detection unit according to theinvention, comprising detectable labels (shaded octagons), polymers(thick lines), a linker (thin line), and a nucleic acid analog segment(shaded bar).

FIG. 2 illustrates an exemplary two-layer method according to theinvention in which a target antigen bound to a primary antibody isrecognized by a recognition unit comprising a secondary antibody probe.The recognition unit is specifically hybridized to a detection unit viathe nucleic acid analog segments on each unit.

FIG. 3 illustrates an exemplary three-layer method according to theinvention wherein a target antigen bound to a primary antibody isrecognized by a recognition unit comprising a secondary antibody probeand a nucleic acid analog segment. The recognition unit specificallyhybridizes to an adaptor unit comprising nucleic acid analog segmentsthat specifically hybridize to the recognition unit and a detectionunit.

FIG. 4 shows another embodiment according to the invention in which atarget antigen is recognized by a recognition unit comprising a primaryantibody probe and a nucleic acid analog segment, wherein the nucleicacid analog segment specifically hybridizes to another nucleic acidanalog segment on a detection unit.

FIG. 5 shows an embodiment wherein a target antigen is recognized by arecognition unit comprising a primary antibody probe and multiplenucleic acid analog segments. Each recognition unit is capable ofhybridizing to at least one detection unit.

FIG. 6 illustrates two methods of enhancing the signal from a targetaccording to the invention. In FIG. 6a , a target antigen is recognizedby a recognition unit comprising a primary antibody as probe and twonucleic acid analog segments. The nucleic acid analog segmentsspecifically hybridize to two detection units comprising detectablelabels (shaded circles). In FIG. 6b , the recognition unit comprises asecondary antibody as probe, which recognizes a primary antibody boundto the target. In FIGS. 6a and 6b , further nucleic acid analog segmentson the detection units shown in different shading may serve tospecifically hybridize to other detection units, for example, to furtheramplify the signal.

FIG. 7 shows two exemplary embodiments according to the invention fordetection of nucleic acid segments. FIG. 7a illustrates a two-layersystem in which a target nucleic acid segment is recognized by arecognition unit comprising a nucleic acid or nucleic acid analog asprobe and a nucleic acid analog segment that specifically hybridizes toa detection unit. The detection unit comprises multiple fluorophores(flower shapes) conjugated to a polymer (thick line) via several linkers(thin lines). FIG. 7b illustrates a three-layer system in which therecognition unit specifically hybridizes to an adaptor unit comprisingseveral nucleic acid analog segments, which in turn, serve to linkseveral detection units to the recognition unit and the target in orderto further enhance the signal from the target.

FIG. 8 illustrates two other embodiments according to the invention inwhich the recognition unit comprises several nucleic acid analogsegments. FIG. 8a shows an exemplary two-layer system such that therecognition unit comprises three different nucleic acid analog segments.FIG. 8b shows an exemplary three-layer system with an alternativerecognition unit comprising three different nucleic acid analogsegments, each attached to the probe via different linkers. Thesearrangements allow a single recognition unit to specifically hybridizeto several different adaptor units as well as many different detectionunits, allowing for different methods of enhancing the signal.

FIG. 9 shows an exemplary multiple-layer system according to theinvention comprising two adaptor units, each with multiple nucleic acidanalog segments.

FIG. 10 also shows an exemplary multiple-layer system according to theinvention comprising two adaptor units, each with multiple nucleic acidanalog segments.

FIG. 11 demonstrates an embodiment according to the invention whereinthe recognition unit comprises multiple nucleic acid analog segments,allowing the recognition unit to specifically hybridize to severaladaptor units, which in turn, specifically hybridize to severaldetection units in order to enhance the signal from the target. (CompareFIG. 11 to FIG. 10, which shows an alternative embodiment generating asimilar level of signal enhancement using two adaptor units rather thanone.)

FIG. 12 shows an embodiment according to the invention comprising morethan one detection unit, each comprising a different detectable label(differently-shaded flower shapes). In that system, the differentnucleic acid analog segments of the adaptor unit specifically hybridizeto each of the different detection units.

FIG. 13 illustrates an embodiment which may allow for visualization ofmore than one target in a sample, such as, here, two different proteinsand a DNA segment. In this embodiment, three different two-layersystems, each comprising a recognition unit and a detection unit areemployed together. Each detection unit carries a different detectablelabel such that the detectable labels are distinguishable from eachother. Each set of recognition unit and detection unit does notcross-react with the other sets or with any other probes or targets inthe sample.

FIG. 14 shows another embodiment according to the invention which mayrecognize multiple targets in a sample. In this example, an adaptor unitis added to one set of recognition and detection units, for example, toenhance the signal from the third target. Such a system may be employed,for example, to adjust the signal intensity of the third target comparedto the other targets in the sample.

FIG. 15 illustrates an embodiment in which three different targets in asample are labeled with the same detectable label, but with differentrecognition units and optional adaptor units.

FIG. 16 shows an embodiment according to the invention in which severaldifferent nucleic acid targets are detected within the same sample. Thetwo or three-layer systems shown allow for adjustments of the signalintensity from the detectable labels, for example, to compensate fordifferences in the natural intensity of each label.

FIG. 17 illustrates an embodiment in which different targets within thesame sample are detected using different detectable labels, in eachcase, using a different method to enhance the signal. For the firsttarget, the recognition unit comprises multiple nucleic acid analogsegments, while for the second target, the recognition unit comprisesonly one nucleic acid analog segment and an adaptor unit comprisingmultiple nucleic acid analog segments is used instead.

FIG. 18 (a-r): Examples of non-natural bases that may be used in thenucleic acid analog segments of the invention, and their names andsymbols.

Where:

-   R1 denotes the attachment point to the backbone-   R2 is, for example, substituents in the 8-position of purines: such    as hydrogen, halogens, or other small substituents i.e., methyl,    ethyl.-   R3 is, for example, substituents on hydrogen bonding exocyclic amino    groups on bases other than cytosine: such as hydrogen, methyl,    ethyl, acetyl.-   R4 is, for example, substituents that face a carbonyl in place of an    aminogroup: such as hydrogen, fluorine and chlorine.-   R5 is, for example, substituents in the 5-position of pyrimidines:    for example, fluorofors, hydrogen, halogens, and substituted and    unsubstituted groups of C1-C20. This position, for example, allows    bulky substituents, if desired.-   R6 is, for example, substituents on the hydrogen bonding excocylic    amino group of cytosine. This position also allows bulky    substituents, for example, alkyl, acyl, and substituted and    unsubstituted groups of C1-C20.

FIG. 19 shows interactions between each of the 18 bases shown in FIG. 1:3 refers to three hydrogen bonds being present between the bases; 2refers to two hydrogen bonds being present between the bases; 1 is thepresence of one hydrogen bond; and X is a repulsion or no H bondingbetween the pairs. There are 3 three bond base pairs, 12 two bond basepairs, and 2 single bond base pairs. As may be seen from the figure andthe text below, these pairing schemes may be used to expand the normalgenetic code and thus may allow nucleic acid analog segments tospecifically hybridize to more than one other nucleic acid analogsegment within the instant recognition, adaptor, and detection units ofthe invention.

FIG. 20 depicts yet other non-natural bases and base-pairings that maybe used in the inventive compositions and methods.

See U.S. Provisional Application No. 60/695,409, and a relatedco-pending International Application entitled “New Nucleic Acid BasePairs” for additional information on these non-natural pairing schemesboth of which are hereby incorporated by reference herein.

DETAILED DESCRIPTION OF THE INVENTION A. Definitions

Sample, as used herein, refers to any composition potentially containinga target.

Target, as used herein, refers to any substance present in a sample thatis capable of detection.

According to this invention, a recognition unit, is a substance thatrecognizes at least one target in a sample. In some embodiments, therecognition unit comprises a probe, which, as defined herein, comprisesany substance that is capable of recognizing a target. In someembodiments of this invention, a recognition unit also comprises atleast one nucleic acid analog segment. In some embodiments, therecognition unit may also comprise at least one polymer and/or at leastone linker.

The terms recognize, recognition, or recognizing, etc., as used herein,mean an event in which one substance, such as a probe or recognitionunit comprising a probe, directly or indirectly interacts with a targetin any way such that the interaction with the target may be detected bya detection unit. In some non-limiting examples, a probe may react witha target, or directly bind to a target, or indirectly react with or bindto a target by directly binding to another substance that in turndirectly binds to or reacts with a target.

As used herein, a detection unit refers to a substance comprising atleast one detectable label, and capable of binding directly to arecognition unit or indirectly to a recognition unit through an optionaladaptor unit. In some embodiments of this invention, a detection unitalso comprises at least one nucleic acid analog segment. In someembodiments, the detection unit may also comprise at least one polymerand/or at least one linker.

An adaptor unit, as used herein, means a substance that is capable oflinking a recognition unit to a detection unit. In some embodiments ofthis invention, an adaptor unit comprises at least two nucleic acidanalog segments. In some embodiments, the adaptor unit may also compriseat least one polymer and/or at least one linker.

The terms specifically hybridizes, specific hybridization, and the like,as used in this application, mean the formation of hydrogen bondsbetween two or more nucleic acid segments or nucleic acid analogsegments under at least low stringency conditions. Non-limiting examplesof the formation of hydrogen bonds between the segments include theformation of Watson-Crick, wobble, and Hoogsteen base-pair geometries,such as to form double strands.

A primary binding agent as used herein, refers to a substance that bindsdirectly to a target in a sample.

A secondary binding agent, as used herein, refers to a substance whichbinds directly to a primary binding agent.

A tertiary binding agent, as used herein, refers to a substance whichspecifically binds a secondary binding agent.

Antibody, as used herein, means an immunoglobulin or a fragment thereof,and encompasses any polypeptide comprising an antigen-binding siteregardless of the source, method of production, and othercharacteristics.

An antigen, as used herein, refers to any substance recognized by anantibody.

According to this invention, a detectable label is any molecule orfunctional group that allows for the detection of the presence of thetarget in the sample.

As used herein, the terms base and nucleobase refer to any purine-likeor pyrimidine-like molecule that may be comprised in a nucleic acidsegment or nucleic acid analog segment.

As used herein, a nucleic acid segment refers to a nucleobase sequencecomprising any oligomer, polymer, or polymer segment, having a backboneformed solely from RNA or DNA nucleosides and comprising only the basesadenine (A), cytosine (C), guanine (G), thymine (T), and uracil (U),wherein an oligomer means a sequence of two or more nucleobases.

A non-natural base, as used herein, means any nucleobase other than:Adenine, A; Guanine, G; Urasil, U; Thymine, T; Cytosine, C.

A non-natural backbone unit includes any type of backbone unit to whicha nucleobase may be attached that is not a ribose-phosphate (RNA) or adeoxyribose-phosphate (DNA) backbone unit.

As used herein, a nucleic acid analog segment means any oligomer,polymer, or polymer segment, comprising at least one monomer thatcomprises a non-natural base and/or a non-natural backbone unit.

As used herein, all numbers are approximate, and may be varied toaccount for errors in measurement and rounding of significant digits.

B. Compositions

1. Recognition, Detection, and Adaptor Units

Certain embodiments of this invention provide compositions useful fordetecting at least one target in a sample. In some embodiments, theinvention provides for a composition comprising a recognition unit and adetection unit wherein:

-   -   a) each unit comprises at least one nucleic acid analog segment;    -   b) at least one nucleic acid analog segment of the recognition        unit specifically hybridizes to at least one nucleic acid analog        segment of the detection unit;    -   c) the recognition unit further comprises at least one probe        which recognizes at least one target in a sample;    -   d) the detection unit further comprises at least one detectable        label; and    -   e) the nucleic acid analog segments on the recognition unit and        detection unit that specifically hybridize to other nucleic acid        analog segments on the recognition unit and detection unit do        not specifically hybridize to the probe, detectable label, or        target. FIGS. 1a and 1c , for example, illustrate exemplary        recognition units and detection units, while other non-limiting        examples are provided in FIGS. 2-17 and elsewhere in the        application as a whole.

Other embodiments of the invention provide for a composition comprisingat least one recognition unit, at least one detection unit, and at leastone adaptor unit, wherein:

-   -   a) each unit comprises at least one nucleic acid analog segment;    -   b) at least one nucleic acid analog segment of the recognition        unit specifically hybridizes to at least one nucleic acid analog        segment of the adaptor unit and at least one nucleic acid analog        segment of the adaptor unit specifically hybridizes to at least        one nucleic acid analog segment of the detection unit;    -   c) the recognition unit further comprises at least one probe        which recognizes at least one target in a sample;    -   d) the detection unit further comprises at least one detectable        label; and    -   e) the nucleic acid analog segments on the recognition unit,        adaptor unit, and detection unit that specifically hybridize to        other nucleic acid analog segments on the recognition unit,        adaptor unit, and detection unit do not specifically hybridize        to the probe, detectable label, or target.

Adaptor units may serve to link recognition units and detection unitstogether. FIG. 1b depicts an exemplary adaptor unit according to theinvention, while other examples are, illustrated in FIGS. 3, 5-12, and14-17, and throughout the application as a whole.

In some embodiments, an adaptor unit has two nucleic acid analogsegments, one to hybridize specifically to a recognition unit andanother to hybridize specifically to a detection unit. In otherembodiments, an adaptor unit has more than two nucleic acid analogsegments, either multiple segments of the same sequence or multipledifferent sequences. In some embodiments, the adaptor units may furtherbe used to link one type of recognition unit to more than one differentdetection unit, or vice versa. For example, in some embodiments,adaptors may function as “master keys” to connect one recognition unitto several different detector units, for instance, detection units withdifferent kinds of detectable labels. Alternatively, adaptor units maylink one detector unit to several different kinds of recognition units,and thus to several different kinds of probes. In other embodiments,adaptor units may also serve to enhance the signal from recognition of atarget. For instance, an adaptor unit with several copies of the samenucleic acid analog segment may specifically hybridize to severaldetector units, thus increasing the number of detectable labels linkedto a given target in a sample.

In certain embodiments, two or more of the recognition, adaptor, anddetection units may be pre-hybridized prior to bringing the compositioninto contact with the sample.

2. Nucleic Acid Analog Segments

The nucleic acid analog segments present on the recognition, detection,and optional adaptor units may comprise at least one non-natural baseand/or a non-natural backbone unit within the segment as a whole. Suchnon-natural units thus include, but are not limited to, for example,PNA's or phosphorothioate or 2′O-methyl nucleosides comprising the oneof the natural bases A, C, G, T, or U, and, for example, natural RNA orDNA nucleosides comprising non-natural base such as 4-thio-Uracil orInosine.

Non-natural bases may include, for example, purine-like andpyrimidine-like molecules, such as those that may interact usingWatson-Crick-type, wobble, or Hoogsteen-type pairing interactions.Examples include generally any nucleobase referred to elsewhere as“non-natural” or as an “analog.”

Examples include: halogen-substituted bases, alkyl-substituted bases,hydroxy-substituted bases, and thiol-substituted bases, as well as5-propynyl-uracil, 2-thio-5-propynyl-uracil, 5-methylcytosine,isoguanine, isocytosine, pseudoisocytosine, 4-thiouracil, 2-thiouraciland 2-thiothymine, inosine, 2-aminopurine, N9-(2-amino-6-chloropurine),N9-(2,6-diaminopurine), hypoxanthine, N9-(7-deaza-guanine),N9-(7-deaza-8-aza-guanine) and N8-(7-deaza-8-aza-adenine).

Yet other examples include bases in which one amino group with ahydrogen is substituted with a halogen (small “h” below), such as2-amino-6-“h”-purines, 6-amino-2-“h”-purines, 6-oxo-2-“h”-purines,2-oxo-4-“h”-pyrimidines, 2-oxo-6-“h”-purines, 4-oxo-2-“h”-pyrimidines.Those will form two hydrogen bond base pairs with non-thiolated andthiolated bases; respectively, 2,4 dioxo and 4-oxo-2-thioxo pyrimidines,2,4 dioxo and 2-oxo-4-thioxo pyrimidines, 4-amino-2-oxo and4-amino-2-thioxo pyrimidines, 6-oxo-2-amino and 6-thioxo-2-aminopurines, 2-amino-4-oxo and 2-amino-4-thioxo pyrimidines, and6-oxo-2-amino and 6-thioxo-2-amino purines.

For example, some specific embodiments of non-natural bases are thestructures shown in FIG. 18 with the following substituents, which aredescribed in the examples that follow.

Base (Symbol) R2 R3 R4 R5 R6 A H or CH₃ H H isoA H or CH₃ H H D H or CH₃H G H or CH₃ H Gs H or CH₃ H I H or CH₃ H U H or CH₃ U2s H or CH₃ U4s Hor CH₃ C H or CH₃ H Py-2o H or CH₃ H or CH₃ Cs H or CH₃ H isoG H or CH₃H isoGs H or CH₃ H Pu-2o H or CH₃ H isoC H H or CH₃ isoCs H H or CH₃Py-4o H or CH₃ H or CH₃ A H or CH₃ H CH₃ isoA H or CH₃ H CH₃ D H or CH₃CH₃ G H or CH₃ CH₃ Gs H or CH₃ CH₃ I H or CH₃ CH₃ U H or CH₃ U2s H orCH₃ U4s H or CH₃ C H or CH₃ CH₃ Py-2o H or CH₃ H or CH₃ Cs H or CH₃ CH₃isoG H or CH₃ CH₃ isoGs H or CH₃ CH₃ Pu-2o H or CH₃ CH₃ isoC CH₃ CH₃ orCH₃ isoCs CH₃ CH₃ or CH₃ Py-4o H or CH₃ H or CH₃

In other examples, one or more of the H or CH₃ are independentlysubstituted with a halogen such as Cl or F. Other example non-naturalbases and base-pairs are shown in FIG. 20 herein. R₁ or “BB” in thestructures of FIGS. 18-20 may serve as a point of attachment to abackbone group, such as PNA, DNA, RNA, etc.

In some embodiments, the following types of base pairs are used: one ormore of Us:A, T:D, C:G, and P:Gs. In some embodiments, T:A and P:G areused. Still other examples are illustrated in FIGS. 2(A) and 2(B) ofBuchardt et al. (U.S. Pat. No. 6,357,163).

Nucleic acid analog segments also include any oligomer, polymer, orpolymer segment, comprising at least one monomer with a non-naturalbackbone unit: in other words, any backbone unit that is not aphosphoribo (RNA) or a phosphodeoxyribo (DNA) unit. Such non-naturalbackbone units include, but are not limited to, for example PNA's orphosphorothioate or 2′O-methyl backbones. For example, in someembodiments, one or more phosphate oxygens may be replaced by anothermolecule, such as sulfur. In other embodiments, a different sugar or asugar analog may be used, for example, one in which a sugar oxygen isreplaced by hydrogen or an amine, or an O-methyl. In yet otherembodiments, nucleic acid analog segments comprise synthetic moleculesthat can bind to a nucleic acid or nucleic acid analog. For example, anucleic acid analog may be comprised of peptide nucleic acids (PNAs),locked nucleic acids (LNAs), or any derivatized form of a nucleic acid.Such backbone units may be attached to any base, including the naturalbases A, C, G, T, and U, and non-natural bases.

As used herein, “peptide nucleic acid” or “PNA” means any oligomer orpolymer comprising at least one or more PNA subunits (residues),including, but not limited to, any of the oligomer or polymer segmentsreferred to or claimed as peptide nucleic acids in U.S. Pat. Nos.5,539,082, 5,527,675, 5,623,049, 5,714,331, 5,718,262, 5,736,336,5,773,571, 5,766,855, 5,786,461, 5,837,459, 5,891,625, 5,972,610,5,986,053, 6,107,470 6,201,103, 6,228,982 and 6,357,163; all of whichare herein incorporated by reference.

The term PNA also applies to any oligomer or polymer segment comprisingone or more subunits of the nucleic acid mimics described in thefollowing publications: Lagriffoul et al., Bioorganic & MedicinalChemistry Letters, 4: 1081-1082 (1994); Petersen et al., Bioorganic &Medicinal Chemistry Letters, 6: 793-796 (1996); Diderichsen et al.,Tett. Lett. 37: 475-478 (1996); Fujii et al., Bioorg. Med. Chem. Lett.7: 637-627 (1997); Jordan et al., Bioorg. Med. Chem. Lett. 7: 687-690(1997); Krotz et al., Tett. Lett. 36: 6941-6944 (1995); Lagriffoul etal., Bioorg. Med. Chem. Lett. 4: 1081-1082 (1994); Diederichsen, U.,Bioorganic & Medicinal Chemistry Letters, 7: 1743-1746 (1997); Lowe etal., J. Chem. Soc. Perkin Trans. 1, (1997) 1: 539-546; Lowe et al., J.Chem. Soc. Perkin Trans. 11: 547-554 (1997); Lowe et al., J. Chem. Soc.Perkin Trans. 11:555-560 (1997); Howarth et al., J. Org. Chem. 62:5441-5450 (1997); Altmann, K-H et al., Bioorganic & Medicinal ChemistryLetters, 7: 1119-1122 (1997); Diederichsen, U., Bioorganic & Med. Chem.Lett., 8: 165-168 (1998); Diederichsen et al., Angew. Chem. Int. Ed.,37: 302-305 (1998); Cantin et al., Tett. Lett., 38: 4211-4214 (1997);Ciapetti et al., Tetrahedron, 53: 1167-1176 (1997); Lagriffoule et al.,Chem. Eur. J., 3: 912-919 (1997); Kumar et al., Organic Letters 3(9):1269-1272 (2001); and the Peptide-Based Nucleic Acid Mimics (PENAMs) ofShah et al. as disclosed in WO96/04000.

As used herein, the term “locked nucleic acid” or “LNA” means anoligomer or polymer comprising at least one or more LNA subunits. Asused herein, the term “LNA subunit” means a ribonucleotide containing amethylene bridge that connects the 2′-oxygen of the ribose with the4′-carbon. See generally, Kurreck, Eur. J. Biochem., 270:1628-44 (2003).

Nucleic acid segments may be synthesized chemically or producedrecombinantly in cells (see e.g. Sambrook et al. (1989) MolecularCloning: A Laboratory Manual, 2nd ed. Cold Spring Harbor Press). Methodsof making PNAs and LNAs are also known in the art (see e.g. Nielson,2001, Current Opinion in Biotechnology 12:16; Sorenson et al. 2003,Chem. Commun. 7(17):2130).

In certain embodiments, one or more of the recognition, adaptor, anddetection units according to the invention comprise more than onenucleic acid analog segment. The two segments may have the same ordifferent sequences.

Interactions between nucleic acid analog segments according to thisinvention may serve to link a recognition unit to a detector unit,either directly, or through the at least one optional adaptor unit.Different nucleic acid analog segments may hybridize, for instance,using Watson-Crick-type, wobble, or Hoogsteen-type base-pairing.Accordingly, the nucleic acid analog segments comprise sequences whichallow for hybridization to take place at a desired stringency.

In some embodiments, the nucleic acid analog segments may pairspecifically with more that one other nucleic acid analog segment,thereby providing degeneracy to the recognition, detection and/oradaptor units. See, for example, the International Application submittedherewith entitled “New Nucleic Acid Base Pairs,” and see the examplesbelow.

This forms the basis for creating systems in which one nucleic acidanalog segment may function as a “master-key” with the ability tohybridize to many partners, where each partner may also hybridize toseparate nucleic acid analog segments. In that way, for example, a veryversatile and flexible detection system may be constructed in someembodiments that allows the user to choose between visualizing severaltargets via different detectable labels and detection units, or via onlyone detectable label and detection unit.

3. Detectable Labels

A detectable label according to the invention may include any moleculewhich may be detected directly or indirectly so as to reveal thepresence of a target in the sample. In some embodiments of theinvention, a direct detectable label is used. Direct detectable labelsmay be detected per se without the need for additional molecules.Examples include fluorescent dyes, radioactive substances, and metalparticles. In other embodiments of the invention, indirect detectablelabels are used, which require the employment of one or more additionalmolecules. Examples include enzymes that affect a color change in asuitable substrate, as well as any molecule that may be specificallyrecognized by another substance carrying a label or react with asubstance carrying a label. Other examples of indirect detectable labelsthus include antibodies, antigens, nucleic acids and nucleic acidanalogs, ligands, substrates, and haptens.

Examples of detectable labels which may be used in the invention includefluorophores, chromophores, electrochemiluminescent labels,bioluminescent labels, polymers, polymer particles, bead or other solidsurfaces, gold or other metal particles or heavy atoms, spin labels,radioisotopes, enzyme substrates, haptens, antigens, Quantum Dots,aminohexyl, pyrene, nucleic acids or nucleic acid analogs, or proteins,such as receptors, peptide ligands or substrates, enzymes, andantibodies (including antibody fragments).

Some detectable labels according to this invention comprise “colorlabels,” in which the target is detected by the presence of a color, ora change in color in the sample. Examples of “color labels” arechromophores, fluorophores, chemiluminescent compounds,electrochemiluminescent labels, bioluminescent labels, and enzymes thatcatalyze a color change in a substrate. In some embodiments, more thanone type of color may be used, for instance, by attachingdistinguishable color labels to a single detection unit or by using morethan one detection unit, each carrying a different and distinguishablecolor label.

“Fluorophores” as described herein are molecules that emit detectableelectro-magnetic radiation upon excitation with electro-magneticradiation at one or more wavelengths. A large variety of fluorophoresare known in the art and are developed by chemists for use as detectablemolecular labels and can be conjugated to the linkers of the presentinvention. Examples include fluorescein or its derivatives, such asfluorescein-5-isothiocyanate (FITC), 5- (and 6)-carboxyfluorescein, 5-or 6-carboxyfluorescein, 6-(fluorescein)-5- (and 6)-carboxamido hexanoicacid, fluorescein isothiocyanate, rhodamine or its derivatives such astetramethylrhodamine and tetramethylrhodamine-5- (and -6)-isothiocyanate(TRITC). Other example fluorophores that could be conjugated to theinstant linkers include: coumarin dyes such as (diethyl-amino)coumarinor 7-amino-4-methylcoumarin-3-acetic acid, succinimidyl ester (AMCA);sulforhodamine 101 sulfonyl chloride (TexasRed™ or TexasRed™ sulfonylchloride; 5- (and -6)- carboxyrhodamine 101, succinimidyl ester, alsoknown as 5- (and -6)-carboxy-X-rhodamine, succinimidyl ester (CXR);lissamine or lissamine derivatives such as lissamine rhodamine Bsulfonyl Chloride (LisR); 5- (and -6)-carboxyfluorescein, succinimidylester (CFI); fluorescein-5-isothiocyanate (FITC);7-diethylaminocoumarin-3-carboxylic acid, succinimidyl ester (DECCA); 5-(and -6)-carboxytetramethylrhodamine, succinimidyl ester (CTMR);7-hydroxycoumarin-3-carboxylic acid, succinimidyl ester (HCCA);6->fluorescein-5- (and -6)-carboxamido!hexanoic acid (FCHA);N-(4,4-difluoro-5,7-dimethyl-4-bora-3a,4a-diaza-3-indacenepropionicacid, succinimidyl ester; also known as 5,7-dimethylBODIPY™ propionicacid, succinimidyl ester (DMBP); “activated fluorescein derivative”(FAP), available from Molecular Probes, Inc.; eosin-5-isothiocyanate(EITC); erythrosin-5-isothiocyanate (ErlTC); and Cascade™ Blueacetylazide (CBAA) (the O-acetylazide derivative of1-hydroxy-3,6,8-pyrenetrisulfonic acid). Yet other potentialfluorophores useful in this invention include fluorescent proteins suchas green fluorescent protein and its analogs or derivatives, fluorescentamino acids such as tyrosine and tryptophan and their analogs,fluorescent nucleosides, and other fluorescent molecules such as Cy2,Cy3, Cy 3.5, Cy5, Cy5.5, Cy 7, IR dyes, Dyomics dyes, phycoerythrin,Oregon green 488, pacific blue, rhodamine green, and Alexa dyes. Yetother examples of fluorescent labels which may be used in the inventioninclude and conjugates of R-phycoerythrin or allophycoerythrin,inorganic fluorescent labels such as particles based on semiconductormaterial like coated CdSe nanocrystallites.

A number of the fluorophores above, as well as others, are availablecommercially, from companies such as Molecular Probes, Inc. (Eugene,Oreg.), Pierce Chemical Co. (Rockford, Ill.), or Sigma-Aldrich Co. (St.Louis, Mo.).

Examples of polymer particles labels which may be used in the inventioninclude micro particles, beads, or latex particles of polystyrene, PMMAor silica, which can be embedded with fluorescent dyes, or polymermicelles or capsules which contain dyes, enzymes or substrates.

Examples of metal particles which may be used in the invention includegold particles and coated gold particles, which can be converted bysilver stains.

Examples of haptens that may be conjugated in some embodiments arefluorophores, myc, nitrotyrosine, biotin, avidin, strepavidin,2,4-dinitrophenyl, digoxigenin, bromodeoxy uridine, sulfonate,acetylaminoflurene, mercury trintrophonol, and estradiol.

Examples of enzymes which may be used in the invention comprise horseradish peroxidase (HRP), alkaline phosphatase (AP), beta-galactosidase(GAL), glucose-6-phosphate dehydrogenase, beta-N-acetylglucosaminidase,ß-glucuronidase, invertase, Xanthine Oxidase, firefly luciferase andglucose oxidase (GO).

Examples of commonly used substrates for horse radish peroxidase (HRP)include 3,3′-diaminobenzidine (DAB), diaminobenzidine with nickelenhancement, 3-amino-9-ethylcarbazole (AEC), Benzidine dihydrochloride(BDHC), Hanker-Yates reagent (HYR), Indophane blue (IB),tetramethylbenzidine (TMB), 4-chloro-1-naphtol (CN), α-naphtol pyronin(α-NP), o-dianisidine (OD), 5-bromo-4-chloro-3-indolylphosphate (BCIP),Nitro blue tetrazolium (NBT), 2-(p-iodophenyl)-3-p-nitrophenyl-5-phenyltetrazolium chloride (INT), tetranitro blue tetrazolium (TNBT),5-bromo-4-chloro-3-indoxyl-beta-D-galactoside/ferro-ferricyanide(BCIG/FF).

Examples of commonly used substrates for Alkaline Phosphatase includeNaphthol-AS-B1-phosphate/fast red TR (NABP/FR),Naphthol-AS-MX-phosphate/fast red TR (NAMP/FR),Naphthol-AS-B1-phosphate/fast red TR (NABP/FR),Naphthol-AS-MX-phosphate/fast red TR (NAMP/FR),Naphthol-AS-B1-phosphate/new fuschin (NABP/NF), bromochloroindolylphosphate/nitroblue tetrazolium (BCIP/NBT),5-Bromo-4-chloro-3-indolyl-b(beta)-d (delta)-galactopyranoside (BCIG).

Examples of luminescent labels which may be used in the inventioninclude luminol, isoluminol, acridinium esters, 1,2-dioxetanes andpyridopyridazines. Examples of electrochemiluminescent labels includeruthenium derivatives.

Examples of radioactive labels which may be used in the inventioninclude radioactive isotopes of iodide, cobalt, selenium, hydrogen,carbon, sulfur and phosphorous.

In some embodiments the detection unit may comprise from 1 up to 500detectable label molecules. In some embodiments, the detectable label isan enzyme, which may be conjugated to a polymer, such that the number ofenzyme molecules conjugated to each polymer molecule is, for instance, 1to 200, 2 to 50, or 2 to 25. In some embodiments, the detectable labelis a gold particle, a radioactive isotope, or a color label, e.g. a lowmolecular weight fluorochrome, and the number of detectable labelsconjugated to each polymer molecule is, for instance, 1 to 500, or forinstance, 2 to 200. In some embodiments, the detectable label is aprotein fluorochrome and the number of detectable labels conjugated toeach polymer molecule is 1-50, 2-20. In some embodiments, the number ofdetectable label molecules conjugated to each polymer is 1-200, 2-50,2-25, or is 10-20, 5-10, or 1-5.

The detectable label can be detected by numerous methods, including, forexample, reflectance, transmittance, light scatter, optical rotation,and fluorescence or combinations hereof in the case of optical labels orby film, scintillation counting, or phosphorimaging in the case ofradioactive labels. See, e.g., Larsson, 1988, Immunocytochemistry:Theory and Practice, (CRC Press, Boca Raton, Fla.); Methods in MolecularBiology, vol. 80 1998, John D. Pound (ed.) (Humana Press, Totowa, N.J.).In some embodiments, more than one detectable label is employed.

When more than one color label is used, the different colors may havedifferent, distinguishable colors. In some embodiments both colors canbe detected simultaneously, such as by fusion or juxtaposition of thesignals, signal enhancement or quenching, or detection of multiplecolors in the sample. The exact choice of detectable label orcombinations of detectable labels may be based on personal preferencesin combinations with restrictions of the sample type, sample preparationmethod, detection method and equipment, and optional contrasting labelsused in the sample.

4. Probes

The instant invention is further compatible with a variety of types ofprobes, including molecules capable of recognizing a target in a sampleeither directly or indirectly through another binding agent. In someembodiments, recognition takes place through binding, while in otherembodiments, recognition takes place through a chemical reaction oranother change in the sample caused by the presence of the target andprobe. In some embodiments, the recognition may be direct, such asthrough non-covalent or covalent binding or reaction between the probeand the target. In other embodiments, the recognition may be indirect,such as through a primary binding agent, or higher level binding agent.For example, in some embodiments, the probe may bind to a primarybinding agent, which in turn binds to a target, or a probe may bind to asecondary binding agent, which binds to a primary binding agent, whichbinds to a target, and so on. In some embodiments, the probe comprises anucleic acid segment, nucleic acid analog segment, protein (including,for instance, an antibody, receptor protein, or enzyme), ligand,receptor, substrate, or hapten.

5. Binding Agents

In certain embodiments, the invention comprises at least one bindingagent, such as a primary binding agent which directly binds to a targetin a sample. In embodiments comprising one or more binding agents, theprobe may directly bind to one or more of the binding agents rather thanto the target itself. In other embodiments, the primary binding agent isan antibody, i.e., a primary antibody. In other embodiments the primarybinding agent is a nucleic acid segment or nucleic acid analog segment.In yet other embodiments the primary binding agent is a receptor,hapten, substrate, or a ligand.

Other embodiments of the invention further comprise a secondary bindingagent. The secondary binding agent may be any molecule that binds theprimary binding agent. For example, in some embodiments the primarybinding agent is a primary antibody. In those embodiments, the secondarybinding agent may comprise e.g. a secondary antibody, a Fc receptor orC1q, a protein from the classical pathway of the complement cascade.Depending on the primary binding agent, the secondary binding agent maybe e.g. an anti-hapten antibody, an MHC molecule, such as an MHC class Iand MHC class II and non conventional MHC, a molecule having a specificbinding partner, such as molecules involved in cellular signalingpathways or molecules having leucine zipper domains, e.g., fos/jun, myc,GCN4, molecules having SH1 or SH2 domains, such as Src or Grb-2. Asecondary binding agent may also be comprised of a chimeric or a fusionprotein, i.e., a protein engineered to combine the features of two ormore specific binding partners. For instance, a leucine zipper could beengineered into an Fc region of an antibody or an SH2 domain could beengineered to be expressed in an Fc region of an antibody. The secondarybinding agent may also comprise a hapten, such as fluorophores, myc,nitrotyrosine, biotin, avidin, strepavidin, 2,4-dinitrophenyl,digoxigenin, bromodeoxy uridine, sulfonate, acetylaminoflurene, mercurytrintrophonol, and estradiol. The secondary binding agent may comprise anucleic acid molecule that specifically hybridizes to a complementarynucleic acid molecule of the primary binding agent.

Yet other embodiments of the invention may comprise a tertiary bindingagent that binds the secondary binding agent. The tertiary binding agentmay comprise, for example, a tertiary antibody or a nucleic acidmolecule or any of the specific binding partners described above for thesecondary binding agent, so long as it specifically binds the secondarybinding agent. Certain embodiments of the invention may further compriseadditional forth, fifth, or even higher order, binding agents similar tothe binding agents described above.

6. Antibodies as Detectable Labels, Binding Agents, and Probes

Antibodies may be used as detectable labels, binding agents, or probes,for example, in various embodiments of this invention. Some embodimentsmay comprise, for example, polyclonal, monoclonal, monospecific,polyspecific, humanized, single-chain, chimeric, synthetic, recombinant,hybrid, mutated, and CDR-grafted antibodies. Various techniques forproducing antibodies and preparing recombinant antibody molecules areknown in the art and have been described, see, e.g., Kohler andMilstein, (1975) Nature 256:495; Harlow and Lane, Antibodies: aLaboratory Manual, (1988) (Cold Spring Harbor Press, Cold Spring Harbor,N.Y.). Antibodies used in the invention may be derived from any mammalspecies, e.g., rat, mouse, goat, guinea pig, donkey, rabbit, horse,lama, camel, or any avian species e.g., chicken, duck. The origin of theantibody is defined by the genomic sequence irrespective of the methodof production.

The antibody may be of any isotype, e.g., IgG, IgM, IgA, IgD, IgE or anysubclass, e.g., IgG1, IgG2, IgG3, IgG4. The skilled artisan willappreciate that antibodies produced recombinantly, or by other means,for use in the invention include any antibody fragment which can stillbind antigen, e.g. an Fab, an F(ab)₂, Fv, scFv. In certain embodiments,the antibody, including an antibody fragment, may be recombinantlyengineered to include a hapten, e.g., a peptide. In certain embodimentsthe hapten may be a myc tag (see FIG. 1N). Inclusion of a hapten in anantibody or antibody fragment facilitates subsequent binding of abinding agent, probe, or label

Certain embodiments employ a primary antibody containing an antigenbinding region which can specifically bind to an antigen target in asample, such as an IHC sample. Thus, a primary antibody may act aseither a primary binding agent or a probe in such embodiments, bydirectly recognizing the antigen target.

Some embodiments further employ a secondary antibody containing anantigen binding region which specifically binds to the primary antibody,e.g., the constant region of the primary antibody. In certainembodiments, the secondary antibody is conjugated to a polymer. In someembodiments, the polymer is conjugated with 2-20 secondary antibodies.In other embodiments, the polymer is conjugated with 2-10 secondaryantibodies. In other embodiments, the polymer is conjugated with 1-5tertiary antibodies, such as 1, 2, 3, 4, or 5. In some such embodiments,the secondary antibody acts as a secondary binding agent, while in othersuch embodiments, the secondary antibody acts as a probe, recognizingthe target antigen indirectly through a primary antibody.

Some embodiments also employ a tertiary antibody containing an antigenbinding region which specifically binds to the secondary antibody, e.g.,a constant region of the secondary antibody, or a hapten linked to thesecondary antibody or a polymer conjugated to the secondary antibody. Incertain embodiments, the tertiary antibody is conjugated to a polymer.In some embodiments, the polymer is conjugated with 1-20 tertiaryantibodies. In other embodiments, the polymer is conjugated with 1-5tertiary antibodies, such as 1, 2, 3, 4, or 5. In some such embodiments,the tertiary antibody acts as a tertiary binding agent, while in othersuch embodiments, the tertiary antibody acts as a probe, recognizing thetarget antigen indirectly through a primary and a secondary antibody.

7. Hybridization of Nucleic Acids and Nucleic Acid Analog Segments

Two different nucleic acid analog segments on the recognition unit,detection unit, and/or adaptor unit may specifically hybridize. In someembodiments, the chosen hybridization conditions are “stringentconditions,” meaning herein conditions for hybridization and washesunder which nucleotide sequences that are significantly complementary toeach other remain bound to each other. The conditions are such thatsequences at least 70%, at least 80%, at least 85-90% complementaryremain bound to each other. The percent complementary is determined asdescribed in Altschul et al. (1997) Nucleic Acids Res. 25:3389-3402(hereby incorporated by reference).

Specified conditions of stringency are known in the art and can be foundin Current Protocols in Molecular Biology, John Wiley & Sons, Inc.(Ausubel et al. 1995 eds.), sections 2, 4, and 6 (hereby incorporated byreference). Additionally, specified stringent conditions are describedin Sambrook et al. (1989) Molecular Cloning: A Laboratory Manual, 2nded. Cold Spring Harbor Press, chapters 7, 9, and 11 (hereby incorporatedby reference).

In other embodiments, the chosen hybridization conditions are “highstringency conditions.” An example of high stringency hybridizationconditions is hybridization in 4× sodium chloride/sodium citrate (SSC)at 65-70° C. or hybridization in 4×SSC plus 50% formamide at 42-50° C.,followed by one or more washes in 1×SSC, at 65-70° C. It will beunderstood that additional reagents may be added to hybridization and/orwash buffers, e.g., blocking agents (BSA or salmon sperm DNA),detergents (SDS), chelating agents (EDTA), Ficoll, PVP, etc.

In yet other embodiments, the chosen conditions are “moderatelystringent conditions.” Moderate stringency, as used herein, includesconditions that can be readily determined by those having ordinary skillin the art based on, for example, the length of the nucleic acid analogsegment. Exemplified conditions are set forth by Sambrook et al.Molecular Cloning: A Laboratory Manual, 2d ed. Vol. 1, pp. 1.101-104,Cold Spring Harbor Laboratory Press (1989) (hereby incorporated byreference), and include use of a prewashing solution of 5×SSC, 0.5% SDS,1.0 mM EDTA (pH 8.0), hybridization conditions of 50% formamide, 6×SSCat 42° C. (or other similar hybridization solution, such as Stark'ssolution, in 50% formamide at 42° C.), and washing conditions of 60° C.,0.5×SSC, 0.1% SDS.

In some embodiments, the chosen conditions are “low stringency”conditions. Low stringency conditions may include, as used herein,conditions that can be readily determined by those having ordinary skillin the art based on, for example, the length of the nucleic acid analogsegment. Low stringency may include, for example, pretreating thesegment for 6 hours at 40° C. in a solution containing 35% formamide,5×SSC, 50 mM Tris-HCl (pH 7.5), 5 mM EDTA, 0.1% PVP, 0.1% Ficoll, 1%BSA, and 500 μg/ml denatured salmon sperm DNA. Hybridizations arecarried out in the same solution with the following modifications: 0.02%PVP, 0.02% Ficoll, 0.2% BSA, 100 μg/ml salmon sperm DNA, 10% W/V dextransulfate, and 5-20×10⁶ CPM probe is used. Samples are incubated inhybridization mixture for 18-20 hours at 40° C., and then washed for 1.5h at 55° C. in a solution containing 2×SSC, 25 mM Tris-HCl (pH 7.4), 5mM EDTA, and 0.1% SDS. The wash solution is replaced with fresh solutionand incubated an additional 1.5 h at 60° C.

These different sets of hybridization conditions may also be used when anucleic acid segment or nucleic acid analog segment is used as a bindingagent, a probe, or a detection label.

8. Polymers

One or more of the recognition unit, detection unit, and adaptor unitmay also comprise at least one polymer. A “polymer,” as used herein, maybe any molecule that facilitates covalent or non-covalent attachment ofone or more other components of a recognition unit, detection unit,and/or adaptor unit. For instance, the polymer may facilitate theattachment of one or more probes, nucleic acid analog segments, and ordetectable labels. The polymer may be a soluble molecule or an insolublemolecule and may have any shape including a linear polymer, branchedpolymer, bead or other globular shaped polymer.

Examples of suitable polymers include polysaccharides such as dextrans,carboxy methyl dextran, dextran polyaldehyde, carboxymethyl dextranlactone, and cyclodextrins; pullulans, schizophyllan, scieroglucan,xanthan, gellan, O-ethylamino guaran, chitins and chitosans such as6-O-carboxymethyl chitin and N-carboxymethyl chitosan; derivatizedcellolosics such as carboxymethyl cellulose, carboxymethyl hydroxyethylcellulose, hydroxyethyl cellulose, 6-amino-6-deoxy cellulose andO-ethylamine cellulose; hydroxylated starch, hydroxypropyl starch,hydroxyethyl starch, carrageenans, alginates, and agarose; syntheticpolysaccharides such as ficoll and carboxymethylated ficoll; vinylpolymers including poly(acrylic acid), poly(acryl amides), poly(acrylicesters), poly(2-hydroxy ethyl methacrylate), poly(methyl methacrylate),poly(maleic acid), poly(maleic anhydride), poly(acrylamide),poly(ethyl-co-vinyl acetate), poly(methacrylic acid),poly(vinylalcohol), poly(vinyl alcohol-co-vinyl chloroacetate), aminatedpoly(vinyl alcohol), and co block polymers thereof; poly ethylene glycol(PEG) or polypropylene glycol or poly(ethylene oxide-co-propyleneoxides) containing polymer backbones including linear, comb-shaped orhyperbranched polymers and dendrimers, including branchedPAMAM-dendrimers; poly amino acids including polylysines, polyglutamicacid, polyurethanes, poly(ethylene imines), pluriol; proteins includingalbumins, immunoglobulins, and virus-like proteins (VLP), andpolynucleotides, DNA, PNA, LNA, oligonucleotides and oligonucleotidedendrimer constructs. Also contemplated is the use of mixed polymers,i.e., a polymer comprised of one or more of the above examples includingany of the polymers, the co-block polymers and random co-polymers.

Properties of the polymer can be varied, depending on the desiredapplication, to optimize performance. Examples of parameters that may beconsidered in the choice of a polymer include the length of the polymerand branching of the polymer. Furthermore, the polymer may carry varioussubstituents. The substituents may be chemically protected and/oractivated, allowing the polymer to be derivatized further.

9. Linkers

The recognition units, detection units, and adaptor units of the presentinvention may also comprise one or more linkers. A “linker,” as usedherein, is a molecule that may help to join other atoms, molecules, orfunctional groups together through chemical bonds. In the instantapplications for example, a linker may serve to join various componentsof each of the units together, such as probes, nucleic acid analogsegments, polymers, and detectable labels.

In some embodiments, the linker also is of sufficient length or sizesuch that the various parts, though chemically attached together,nonetheless remain separated from each other in space, thus minimizingsteric clashes. For instance, a linker on a recognition unit may serveto join a probe to a nucleic acid analog segment, while separating themsufficiently to avoid steric clashes. A linker may also serve toseparate a polymer from another component of one of the units such as anucleic acid analog segment, to separate two or more nucleic acid analogsegments, or to separate a detectable label from a nucleic acid analogsegment, or to separate multiple probes or multiple detectable labels.Linkers may also increase the solubility of the conjugates and mayprevent unwanted interactions by shielding the components and maythereby confer a general and significant lower non-specific backgroundfor the visualization system.

Reducing the steric hindrance between the various components of thedifferent units of the composition may also improve detectionefficiency. For example, certain detection labels show reduced signalswhen in close proximity to other detection labels. Fluorescent labels,for instance, may become quenched if present in close proximity.Further, reducing steric hindrance increases the binding affinity of thevarious components for their intended binding partners and decreases thelevel of the background and the risk of false positive signals.

A person of ordinary skill in the art of molecular conjugation knowsnumerous linkers. Examples include 6-amino-hexanoic acid, succimidyl4-(N-maleimidomethyl) cyclohexane-1-carboxylate (SMCC), homobifunctionallinkers such as divinyl sulfone (DVS), glutaric dialdehyde, hexanedi-isocyanate, dimethylapimidate, 1,5-difluoro-2,4-dinitrobenzene,heterobifunctional linkers like e.g. N-gamma-maleimidobytyroloxysuccinimide ester (GMBS), and zero length linkers such as1-ethyl-3-(3-dimethylaminopropyl)carbodiimide

Longer linker molecules based upon polyethylene glycol (PEG) are alsoavailable in the art. (See, for example, Discrete PEG (dPEG)™modification reagents available from Quanta Biodesign, Ltd., Powell,Ohio, or at www.quantabiodesign.com; PEG-based reagents available fromEMD Biosciences, Inc., San Diego, Calif., described in NovabiochemApril, 2004, “Product focus: PEG reagents—bifunctional amino-PEG-acidspacers” brochure, available at www.novabiochem.com; and see Baumeisteret al., Biopolymers, 71: 339 (2003); Kumar & Aldrich, Org. Lett., 5: 613(2003). (See also, “Chemistry of Protein Conjugation and Cross-Linking”Shan S. Wong CRC Press, Boca Raton, Fla., USA, 1993; “BioConjugateTechniques” Greg T. Hermanson Academic Press, San Diego, Calif., USA,1996; “Catalog of Polyethylene Glycol and Derivatives for AdvancedPEGylation, 2004” Nektar Therapeutics Inc, Huntsville, Ala., USA).

The present invention may also use a long uncharged linker comprising atleast two units of the Formula I.

In Formula I, R₁ and R₂ may comprise either NH or O, while R₃ maycomprise methyl, ethyl, propyl, CH₂—O—CH₂, and (CH₂—O—CH₂)₂. Forexample, in some embodiments of the instant invention, the linkercomprises at least two units of the Formula I wherein R₁ and R₂ are bothNH and R₃ is CH₂—O—CH₂. See the examples that follow and theaccompanying International Application entitled “MONOMERIC AND POLYMERICLINKERS USEFUL FOR CONJUGATING BIOLOGICAL MOLECULES AND OTHERSUBSTANCES” for further description of this linker.

C. Methods of Making Compositions According to the Invention

The recognition units, detection units, and adaptor units according tothe invention may comprise, for example, molecules in which the variouscomponents such as probes, detection labels, nucleic acid analogsegments, linkers, and polymers are covalently attached to formconjugates. As used herein, the terms “conjugate, conjugation” and thelike refer to the formation of covalent attachments between varioussubstances, either directly without intervening bonds, or indirectlythrough at least one intervening bond. Alternatively, in someembodiments, the components of each unit may be attached through stable,non-covalent interactions such as base-pairing, adsorption,intercalation, and similar hydrogen bonding, van der Waals, orhydrophobic interactions, that are sufficiently stable under conditionsof use.

Many methods of conjugating molecules are known in the art and can beused to make the various units of the invention. For example, conjugatescomprising a linker or polymer according to this invention may be formedby covalently coupling amino groups to conjugated double bonds on apolymer or linker. In one embodiment the polymer is activated withdivinylsulfone and mixed with a probe, nucleic acid analog segment,and/or detectable label to form a polymer conjugate. In otherembodiments, aldehydes may be used to activate a polymeric backbone. Forinstance, dextrans may then be mixed with the binding agent and anoptional detectable label. Yet another method of preparing polymericconjugates is by using so called chemo-selective schemes for couplingthe components together, e.g., enzymes or other molecules can bederivatized with thiol-reactive maleimide groups before being conjugatedto a thiol-modified polymeric carrier or backbone.

In some embodiments no exogenous polymeric backbone is required forattachment of a probe, detectable label, and/or nucleic acid analogsegment to one of the instant units. In these embodiments, thecomponents themselves may be activated for conjugation or may beself-polymerizable. For example, a vinyl group may be used to activatethe components for conjugation. Polymerization then occurs by additionof a radical, which results in polymerization of the vinyl groups toform a polymeric conjugate. The conjugate thus will contain a poly vinylbackbone or blocks of poly vinyl. Alternatively, active esters ofacrylic acid can be used to activate proteins and other molecules.Generation of free radicals can polymerize the derivatized molecules.Small molecule linkers with more than one vinyl group can be furtheradded to help form a polymeric conjugate.

In some embodiments, the components may be organized in the unit withthe help of one or more linkers, as described above. Many such linkersare known in the art and available commercially, as described, and thelinkers may be activated for attachment to other components of the unitsaccording to the invention according to methods available fromcommercial suppliers or in the literature. See the examples that follow,U.S. Provisional Application Nos. 60/695,408; 60/695,409; and 60/695,410and the International Application entitled “MONOMERIC AND POLYMERICLINKERS USEFUL FOR CONJUGATING BIOLOGICAL MOLECULES AND OTHERSUBSTANCES,” for examples.

D. Methods

1. General Detection Methods

Some embodiments of the invention comprise methods of detecting a targetin a sample comprising:

-   -   a) contacting a sample possibly comprising the target with at        least one recognition unit comprising at least one probe, such        that the probe recognizes the target to form a first complex,        -   wherein the recognition unit further comprises at least one            nucleic acid analog segment;    -   b) contacting the first complex of (a) with at least one        detection unit comprising at least one nucleic acid analog        segment and at least one detectable label,        -   wherein at least one nucleic acid analog segment of the            recognition unit specifically hybridizes to at least one            nucleic acid analog segment of the detection unit to form a            second complex,        -   and wherein the nucleic acid analog segments on the            recognition unit and the detection unit that hybridize to            each other do not specifically hybridize to the probe,            detectable label, or target;    -   c) detecting the second complex of (b); and    -   d) optionally comparing the signal from the target in the sample        with the signal from a reference target or reference sample.

In some embodiments, the detection and/or recognition units may comprisemore than one probe, detectable label, nucleic acid analog segment,polymer, or linker. For example, in FIGS. 2 and 4, multiple detectablelabels are attached to the detection unit via a polymer.

In some embodiments, a recognition unit may comprise a probe thatdirectly binds to the target, as shown in FIG. 4, for example. In otherembodiments, the probe may recognize the target by binding to itindirectly, as shown in FIG. 2, in which the probe is a secondarybinding agent (e.g. a secondary antibody) that binds to a primarybinding agent (e.g. a primary antibody) that in turn directly binds tothe target. Such a system may allow for an enhancement of the signal,if, for example, each primary binding agent may be bound to more thanone secondary binding agent acting as a probe. If more than one proberecognizes a target, more than one detection unit may become associatedwith a target, for example. Compare, for example, FIG. 2 to FIG. 4.

In some embodiments of the invention, an optional adaptor unit is usedwhich serves to join the recognition units and detection units. In someembodiments, the invention provides a method of detecting a target in asample comprising:

-   -   a) contacting a sample possibly comprising the target with at        least one recognition unit comprising at least one probe and at        least one nucleic acid analog segment, such that the probe        recognizes the target to form a first complex;    -   b) contacting the first complex of (a) with at least one adaptor        unit comprising at least two nucleic acid analog segments, such        that the recognition unit and at least one adaptor unit form a        second complex;    -   c) contacting the second complex of (b) with a detection unit        comprising at least one nucleic acid analog segment and at least        one detectable label, such that the detection unit recognizes        the second complex of (b) and forms a third complex,        -   wherein the nucleic acid analog segments comprised on the            recognition unit, adaptor unit, and detection unit that            specifically hybridize to each other do not specifically            hybridize to the probe, detectable label, or target;    -   d) detecting the third complex of (c); and    -   e) optionally comparing the signal from the target with the        signal from a reference target or reference sample.

The adaptor units may create a third “layer” to the detection system,which may merely connect different recognition and detection unitstogether, while in other embodiments, one or more adaptor units may alsoserve to further enhance the signal obtained from the target. Forexample, the adaptor unit may be structured such that it canspecifically hybridize to more than one detection unit, thus increasingthe number of detection units ultimately joined to a target. See, forexample, FIGS. 2 and 3, FIGS. 4 and 5, and FIGS. 7a and 7b . This isuseful, for instance, when the amounts of targets are low or when astrong detection signal is desired. In some embodiments, more than oneadaptor unit may be used in order to create yet additional layersallowing for further adaptability and amplification. See, for example,FIGS. 9, 10, 11, and 12, each of which use two adaptor units.

Multiple nucleic acid analog segments and adaptor units may increase theflexibility of the detection methods as a whole. For instance, by usingan adaptor unit comprising multiple nucleic acid analog segments, onerecognition unit may be able to link to several different detectionunits. Such a system may be useful, for example, to assess a targetpresent in different samples, in which the samples have differentcompositions, or, for example, to switch from one type of detectablelabel to another depending on the sample conditions. For example, inFIG. 8b , an adaptor unit is shown comprising three different nucleicacid analog segments, which may be combined with different sets ofdetection units and recognition units. In other embodiments, such asshown in FIG. 8a , flexibility may be generated without the use of anadaptor unit, such as including multiple nucleic acid analog segmentswithin the recognition unit, either close together as shown in FIG. 8a ,or joined by different linkers, as shown in FIG. 8b . Yet further,multiple probes may also be used, such that a recognition unit binds tomore than one type of target.

The thermodynamics and kinetics of the interactions of the differentunits may also be controlled through the number and sequence of thenucleic acid analog segments as well as through the concentrations ofthe different units. For instance, the binding strength between thedifferent units may be increased using multiple nucleic acid analogsegments. See, for example, FIGS. 10 and 11 in which the adaptor unitsinclude multiple nucleic acid analog segments of the same sequence,creating multiple attachments between the different units. See also FIG.12, in which the second adaptor unit comprises multiple nucleic acidanalog segments of two different sequences, allowing for binding to twodifferent detection units, each detection unit linked to an adaptor unitby multiple attachments.

The invention may also be employed to detect more than one target in asample. In certain embodiments, for example, different targets in thesame sample may be detected with different sets of recognition anddetection units and different detectable labels. See FIG. 13. Forexample, cross-reactivity may be avoided using different sets ofbase-paired nucleic acid analog segments within each of the sets ofrecognition and detection units. Because of the lack of cross-reactivitythat the different specific hybridizations allow, the instant inventionallows for methods in which all of the recognition units and detectionunits are added to the sample at the same time.

In other embodiments, at least one set of target-recognizing anddetecting units may further include at least one adaptor unit. See FIG.14. In some embodiments, the adaptor unit may serve to enhance thesignal from one of the sets of recognition and detection units, forinstance, to compensate for a weaker recognition by a probe, or for alower amount of a target. Hence, the adaptor units according to theinvention may be used in some assays to even out the intensities of thesignals from different targets in the sample.

In yet other embodiments, a flexible system may be generated in whichthe same set of reagents may be used to detect more than one type oftarget. For example, in FIG. 15, three different targets are detectedusing the same detection unit and adaptor unit, but differentrecognition units. In another example shown in FIG. 16, many differenttargets in the same sample, such as nucleic acid segments, may bedetected using the same detection unit and adaptor unit, but differentrecognition units each carrying a different probe. Such a system may beuseful in detecting targets in an array-type sample, for instance. Inpreferable embodiments the method comprises steps of adding a mixture ofprimary binding agents or compositions comprising a mixture of primarybinding agents and steps of adding compositions comprising a mixture ofdetectable labels. In certain embodiments compositions comprising suchmixtures may be designed for multi-purpose use, wherein not all bindingagents binds to a target or another binding agent. Multi-purposecompositions may for example be useful in methods for analysis ofdifferent samples expressing only few of several targets.

In some embodiments of the invention, one or more probes or bindingagents or external components present in a sample may be stericallyhindered. For example, FIG. 17, left panel, illustrates that the abilityof a primary antibody to bind to a target may be reduced by sterichindrance from a conjugated nucleic acid analog segment. Such engineeredsteric hindrance may reduce non-specific binding or cross-reactivity,thus increasing the sensitivity of a system.

Methods according to the invention may also be used for or inconjunction with methods of diagnosing at least one disease orcondition.

Additional applications of the instant methods are described in otherInternational Applications submitted herewith entitled “New Nucleic AcidBase Pairs” and “Monomeric and Polymeric Linkers Useful For ConjugatingBiological Molecules and Other Substances,” the entire disclosures ofwhich are incorporated herein by reference.

2. Targets

The instant invention can be applied to a variety of targets. Any targetwhich can be recognized by a suitable recognition unit and probe iscompatible with the instant invention. In some embodiments, therecognition may be direct, while in other embodiments, the recognitionmay be indirect, via another binding agent, such as at least oneprimary, secondary, or higher order binding agent.

In some embodiments, the target comprises a protein, such as aglycoprotein or lipoprotein, phosphoprotein, methylated protein, or aprotein fragment, a peptide, or a polypeptide. In other embodiments, thetarget comprises a nucleic acid segment. In yet other embodiments, thetarget comprises a nucleic acid analog segment.

In other embodiments, the target may comprise a lipid; a glyco-lipid; asugar; a polysaccharide; a starch; a salt; an ion; or one of a varietyof other organic and inorganic substances; any of which may be free insolution or bound to another substance. The target may be expressed onthe surface of the sample, e.g., such as on a membrane or interface.Alternatively, the target may be contained in the interior of thesample. In the case of a cell sample, for instance, an interior targetmay comprise a target located within the cell membrane, periplasmicspace, cytoplasm, or nucleus, or within an intracellular compartment ororganelle.

Targets may also include viral particles, or portions thereof, e.g., anucleic acid segment or a protein. The viral particle may be a freeviral particle, i.e., not associated with any other molecule, or it maybe associated with any sample described above. In some embodiments, thetarget may be an antigen or an antibody.

3. Detection Systems

The instant invention is compatible with many known detection formatsand their associated samples. For example, the invention may be used inconnection with immunoassays, protein detection assays, or nucleic acidhybridization assays such as: immunohistochemistry (IHC),immunocytochemistry (ICC), in situ hybridization (ISH), flow cytometry,enzyme immuno-assays (EIA), enzyme linked immuno-assays (ELISA),blotting methods (e.g. Western, Southern, and Northern), labeling insideelectrophoresis systems or on surfaces or arrays, and precipitation,among others. All of those detection assays are useful in research aswell as in the detection and diagnosis of a variety of diseases andconditions, for example.

For example, IHC specifically provides a method of detecting targets ina sample or tissue specimen in situ (see Mokry 1996, ACTA MEDICA39:129). The overall cellular integrity of the sample is maintained inIHC, thus allowing detection of both the presence and location of thetargets of interest. Typically a sample is fixed with formalin, embeddedin paraffin and cut into sections for staining and subsequent inspectionby light microscopy. Current methods of IHC use either direct labelingor secondary antibody-based or hapten-based labeling. Examples of knownIHC systems include, for example, EnVision™ (DakoCytomation),Powervision® (Immunovision, Springdale, Ariz.), the NBA™ kit (ZymedLaboratories Inc., South San Francisco, Calif.), HistoFine® (NichireiCorp, Tokyo, Japan). The present invention may allow for enhancement ofsignal or increased flexibility in IHC detection platforms.

IHC, ISH and cytological techniques may be performed in a matrix oftissue, cell and proteins which may be partly cross-linked and veryinhomogeneous in nature. Diffusion rates increase with increasingconcentrations and increasing temperature, but decrease with molecularweight and molecular size. Therefore, the physical size of thecomponents is of great importance. For instance, large molecules can beexcluded from diffusing into parts of the sample whereas small sizedcomponents more easily may diffuse in and out of the differentcompartments of the sample. In some embodiments, the units of theinvention may be designed to be of small size and, for example, smallerthan an antibody or biotin-streptavidine complex, in order to improvetarget recognition and detection.

4. Samples

Many types of samples are compatible with the instant invention. Samplesmay comprise solid and liquid solutions, for example, containing targetsin a buffer. Samples may also be derived from living matter taken fromany living organism, e.g., an animal, such as mammals (e.g. humans),plants, fungi, archaea, or bacteria. Thus, samples may compriseeukaryotic cells, archaeal cells, or prokaryotic cells. Samples maycomprise a cell sample, such as a cell smear or colony, or a tissuespecimen derived from a living organism, such as a tissue sample from anorgan. They may also comprise a biological fluid, such as ananimal-derived fluid, e.g. mammalian plasma, serum, lymph, whole blood,spinal, amniotic, or other fluid. Samples may also comprise othernaturally-obtained samples such as soil or water samples, andsynthetically derived samples such as chemical or industrial products orsolutions, food products, and buffers.

Tissue or cell samples according to the invention may be prepared by avariety of methods known to those of ordinary skill in the art,depending on the type of sample and the assay format. For instance,tissue or cell samples may be fresh or preserved, and may be, forexample, in liquid solution, flash-frozen or lyophilized, smeared ordried, embedded, or fixed on slides or other supports. In someembodiments, samples may be prepared and stained using a free-floatingtechnique. In this method a tissue section is brought into contact withdifferent reagents and wash buffers in suspension or freely floating inappropriate containers, for example micro centrifuge tubes, before beingmounted on slides for further treatment and examination.

In some embodiments, a tissue section may be mounted on a slide or othersupport after an incubation with immuno-specific reagents. The remainsof the staining process are then conducted after mounting. For example,for microscopic inspection in IHC and ISH, samples may be comprised in atissue section mounted on a suitable solid support. For the productionof photomicrographs, sections comprising samples may be mounted on aglass slide or other planar support, to highlight by selective stainingcertain morphological indicators of disease states or detection ofdetectable targets.

In some IHC embodiments, a sample may be taken from an individual, fixedand exposed to, for example, antibodies which specifically bind to thedetectable target of interest. Sample processing steps may include, forexample, antigen retrieval, exposure to a primary antibody, washing,exposure to a secondary antibody (optionally coupled to a suitabledetectable label), washing, and exposure to a tertiary antibody linkedto a detectable label. Washing steps may be performed with any suitablebuffer or solvent, e.g., phosphate-buffered saline, TRIS-bufferedsaline, distilled water. The wash buffer may optionally contain adetergent, e.g., TWEEN® 20 or NP-40.

IHC samples may include, for instance: (a) preparations comprisingun-fixed fresh tissues and/or cells or solution samples (b) fixed andembedded tissue specimens, such as archived material; and (c) frozentissues or cells. In some embodiments, an IHC staining procedure maycomprise steps such as: cutting and trimming tissue, fixation,dehydration, paraffin infiltration, cutting in thin sections, mountingonto glass slides, baking, deparaffination, rehydration, antigenretrieval, blocking steps, applying primary antibody, washing, applyingsecondary antibody—enzyme conjugate, washing, applying a tertiaryantibody conjugated to a polymer and linked with an enzyme, applying achromogen substrate, washing, counter staining, applying a cover slipand microscopic examination.

ISH samples, for instance, may be taken from an individual and fixedbefore being exposed to a nucleic acid or nucleic acid analog probe on arecognition unit. In some embodiments, the nucleic acid in the samplemay first be denatured to expose the target binding sites. Variouscounter-stains or paints may further be used in order to locate nucleicacid molecules or chromosomes within an ISH sample.

5. Quantitation of Signals

In some embodiments, the approximate amount of a target in a sample isalso determined. For instance, a control target within the sample may beassayed as well as an experimental target. In the case of a nucleic acidtarget, for example, a chromosomal paint or counter-stain may be used.For instance, if the target is a locus on a larger piece of nucleic acidsuch as a plasmid or chromosome, the intensity of a contrasting labelfor the plasmid or chromosome or a neutral locus thereon may be comparedto the intensity of the target locus. The intensity of the label fromthe sample may also be compared to that of a known standard or controlsample. Estimating the amount of a detectable target in a sample ishelpful, for instance, in a variety of diagnostic tests, and theestimate may be used to plan a course of treatment for a suspecteddisease or condition. Several commercial densitometry software programsand related instruments are available to quantitate the intensity of astained target in a sample, such as those available from Fuji Film,Applied Biosystems, and Molecular Dynamics.

6. Methods of Fixing Samples

In some embodiments of this invention, tissue or cell samples may befixed or embedded. Fixatives may be needed, for example, to preservecells and tissues in a reproducible and life-like manner. Fixatives mayalso stabilize cells and tissues, thereby protecting them from therigors of processing and staining techniques. For example, samplescomprising tissue blocks, sections, or smears may be immersed in afixative fluid, or in the case of smears, dried.

Many methods of fixing and embedding tissue specimens are known, forexample, alcohol fixation and formalin-fixation and subsequent paraffinembedding (FFPE). Any suitable fixing agent may be used. Examplesinclude ethanol, acetic acid, picric acid, 2-propanol,3,3′-diaminobenzidine tetrahydrochloride dihydrate, acetoin (mixture ofmonomer) and dimer, acrolein, crotonaldehyde (cis+trans), formaldehyde,glutaraldehyde, glyoxal, potassium dichromate, potassium permanganate,osmium tetroxide, paraformaldehyde, mercuric chloride,tolylene-2,4-diisocyanate, trichloroacetic acid, tungstic acid. Otherexamples include formalin (aqueous formaldehyde) and neutral bufferedformalin, glutaraldehyde, carbodiimide, imidates, benzoequinone, osmicacid and osmium tetraoxide. Fresh biopsy specimens, cytologicalpreparations (including touch preparations and blood smears), frozensections, and tissues for IHC analysis may be fixed in organic solvents,including ethanol, acetic acid, methanol and/or acetone.

7. Increasing the Reactivity and Specificity of Detectable Targets

In some embodiments, it may be helpful to pre-treat the samples toincrease the reactivity or accessibility of a detectable target and toreduce non-specific interactions.

If the target is an antigen, for example, a process called “antigenretrieval” may be used (and which is also known in the art as targetretrieval, epitope retrieval, target unmasking, or antigen unmasking).See, e.g., Shi et al., J Histochem Cytochem, 45(3): 327 (1997). Antigenretrieval encompasses a variety of methods including enzymatic digestionwith proteolytic enzymes, such as e.g. proteinase, pronase, pepsin,papain, trypsin or neuraminidase. Some embodiments may use heat, e.g.“heat-induced epitope retrieval” or HIER. Heating may involve amicrowave irradiation, or a water bath, a steamer, a regular oven, anautoclave, or a pressure cooker in an appropriately pH stabilizedbuffer, usually containing EDTA, EGTA, Tris-HCl, citrate, urea,glycin-HCl or boric acid. One may add detergents to the HIER buffer toincrease the epitope retrieval, or to the dilution media and/or rinsingbuffers to lower non-specific binding. In some embodiments, combinationsof different antigen retrieval methods may be used.

The antigen retrieval buffer may be aqueous, but may also contain othersolvents, including solvents with a boiling point above that of watersuch as e.g. glycerol. This allows for treatment of the tissue at morethan 100° C. at normal pressure.

Additionally, in some embodiments, the signal-to-noise ratio may beincreased by different physical methods, including application ofvacuum, or ultrasound, or freezing and thawing tissue samples before orduring incubation of the reagents.

In some embodiments, treatments may be performed to reduce non-specificbinding. For example, carrier proteins, carrier nucleic acid molecules,salts, or detergents may reduce or prevent non-specific binding.Non-specific binding sites may be blocked in some embodiments with inertproteins like, HSA, BSA, ovalbumin, with fetal calf serum or other sera,or with detergents like TWEEN®20, TRITON® X-100, Saponin, BRIJ®, orPLURONICS®. Alternatively, non-specific binding sites may be blockedwith unlabeled competitors for the recognition event between the targetand the probe. For example, in the case of a nucleic acid interaction,non-specific binding may be reduced by adding unlabeled competitornucleic acids or nucleic acid analogs such as digested, total human DNAor salmon sperm DNA, or unlabeled versions of the binding agent. Inaddition, repetitive sequences may be blocked, for example, usingnucleic acids or nucleic acid analogs that specifically recognize thosesequences, or sequences derived from a total DNA preparation. Salt,buffer, and temperature conditions may also be modified so as to reducenon-specific binding.

Cross reactivity of different components of the detection methods may beavoided, for example, by using antibodies derived from differentspecies. Furthermore, combinations of e.g. secondary antibodies againstprimary antibodies and haptens may also be used to avoid unwanted crossreactivity. Alternatively, unwanted cross-reactivity or non-specificbinding may be reduced or eliminated by designing sterically hinderedrecognition units, adaptor units, or detection units. For instance, arecognition unit may be designed such that the nucleic acid analogsegments provide a certain degree of steric hindrance near the probe. Inaddition, one may remove endogenous biotin binding sites or endogenousenzyme activity (for example phosphatase, catalase or peroxidase) as astep in the staining procedure. Endogenous biotin and peroxidaseactivity may be removed by treatment with peroxides, while endogenousphosphatase activity may be removed by treatment with levamisole.Heating may destroy endogenous phosphatase and esterase activity.

E. Kits and Instruments

The invention also provides a kit comprising one or more compositionsaccording to the invention. The kit may optionally comprise one or morebinding agents, and suitable reagents for, for instance: antigenretrieval, sample dilution, reagent dilution, blocking of non-specificbinding, blocking of endogenous enzyme activity, or blocking ofrepetitive sequences. The kit may optionally also comprise at least onecontainer, instructions for use, and reference targets or samples.

Instruments may be used in various embodiments of the invention.Instruments, capable of performing steps of staining, are useful forcarrying out both single as well as multi-staining procedures, and, inparticular, useful for detection of multiple targets that frequentlyrequires balancing of the signals emanating from the differentdetectable labels.

WORKING EXAMPLES Example 1a. Preparation of Pyrimidinone-Monomer

1. In dry equipment 4.6 g of solid Na in small pieces was added to 400mL ethanol (99.9%), and was dissolved by stirring. Hydroxypyrimidinehydrochloride, 13.2 g, was added and the mixture refluxed for 10minutes. Then 12.2 mL ethyl-bromoacetate (98%) was added and the mixturerefluxed for 1½ hour. The reaction was followed using Thin LayerChromatography (TLC). The ethanol was evaporated leaving a whitecompound, which was dissolved in a mixture of 80 mL of 1 M NaCitrate (pH4.5) and 40 mL of 2 M NaOH. This solution was extracted four times with100 mL Dichloromethane (DCM). The DCM phases were pooled and washed with10 mL NaCitrate/NaOH—mixture. The washed DCM phases were evaporatedunder reduced pressure and resulted in 17.2 g of crude solid product.This crude solid product was recrystallized with ethylacetate giving ayellow powder. The yield for this step was 11.45 g (63%).

2. The yellow powder, 12.45 g. from above was hydrolyzed by refluxingovernight in a mixture of 36 mL DIPEA, 72 mL water and 72 mL dioxane.The solvent was evaporated and water was removed from the residue byevaporation from toluene. The yield for this step was 100%.

3. OBS. Pyrimidinone acetic acid (10.5 g), 16.8 g PNA-backboneethylester, 12.3 g DHBT-OH, 19 mL Triethylamine was dissolved in 50 mLN,N-dimethylformamide (DMF). DIPIDIC (11.8 mL) was added and the mixturestirred overnight at room temperature. The product was taken up in 100mL DCM and extracted three times with 100 mL of dilute aqueous NaHCO₃.The organic phase was extracted twice with a mixture of 80 mL of 1 MNaCitrate and 20 mL of 4 M HCl. Because TLC showed that some materialwas in the citrate phase, it was extracted twice with DCM. The organicphases were pooled and evaporated. Because there was a precipitation ofurea, the product was dissolved in a DCM, and the urea filtered off.Subsequent evaporation left an orange oil. Purification of the orangeoil was performed on a silica column with 10% methanol in DCM. Thefractions were collected and evaporated giving a yellow foam. The yieldfor this step was 7.0 g (26.8%).

4. The yellow foam (8.0 g) was hydrolyzed by reflux overnight in 11 mLDIPEA, 22 mL water, and 22 mL dioxane. The solvent was evaporated andthe oil was dehydrated by evaporation from toluene leaving an orangefoam. The yield for this step was 100%.

Example 1b. Second Method of Preparing Pyrimidinone Monomer

Step 1. In dry equipment 9.2 g of solid Na in small pieces was dissolvedin 400 mL ethanol (99.9%), with stirring. Hydroxypyrimidinehydrochlorid, 26.5 g, was added, and the mixture was stirred for 10minutes at 50° C. Then 24.4 mL Ethyl bromoacetate (98%) was added andthe mixture stirred at 50° C. for 1 hour. The reaction was followedusing Thin Layer Chromatography (TLC).

The ethanol was evaporated leaving a white compound, which was dissolvedin 70 mL of water and extracted with 20 mL DCM. Another 30 mL of waterwas added to the water phase, which was extracted with 3×100 mL DCM. TheDCM-phase from the first extraction contains a lot of product, but alsosome impurities, wherefore this phase was extracted twice with water.These two water phases then were back extracted with DCM.

The combined DCM phases were pooled and washed with 10 mL water. Thewashed DCM phases were evaporation under reduced pressure and resultedin 25.1 g yellow powder. The yield for this step was 25.1 g=69%.Maldi-Tof: 181.7 (calc. 182).

Step 2. 34.86 g yellow powder from above was dissolved in 144 mL 2 MNaOH. After stirring 10 minutes at room temperature, the mixture wascooled in an ice bath. Now 72 mL 4 M HCl (cold) was added. The productprecipitated. After stirring for 5 minutes, the precipitate was filteredand thoroughly washed with ice water. Drying in a dessicator underreduced pressure left 18.98 g yellow powder. The yield for this step was18.98 g=64%.

Step 3. Pyrimidinone acetic acid 11.1 g and triethylamine 12.5 mL weredissolved in N,N-dimethylformamide (DMF) 24 ml, HBTU 26.2 g was addedplus 6 mL extra DMF. After 2 minutes a solution of PNA-Backboneethylester 14.7 g dissolved in 15 mL DMF was added. The reaction mixturewas stirred at room temperature and followed using TLC. After 1½ hourprecipitate had formed. This was filtered off.

The product was taken up in 100 mL DCM and extracted with 2×100 mLdilute aqueous NaHCO3. Both of the aqueous phases were washed with alittle DCM. The organic phases were pooled and evaporated. Evaporationleft an orange oil. Purification of the product was done on a silicacolumn with 10-20% methanol in ethylacetate. The fractions werecollected and evaporated giving a yellow oil. The oil was dissolved andevaporated twice from ethanol. The yield from this step was 20.68 g=90%.

Step 4. The yellow oil (18.75 g) was dissolved in 368 mL 0.2 M Ba(OH)2.Stirring for 10 minutes before 333 mL 0.221 M H2SO4 was added. Aprecipitation was performed immediately. Filtration through cellite,which was washed with water. The solvent was evaporated. Before theevaporation was at end, the product was centrifuged to get rid of thevery rest of the precipitation. Re-evaporation of the solvent left ayellow oil. The yield from this step was 13.56 g 78%.

Step 5. To make a test on the P-monomer 3 consecutive P's were coupledto Boc-L300-Lys(Fmoc)-resin, following normal PNA standard procedure.The product was cleaved from the resin and precipitated also followingstandard procedures: HPPP-L300-Lys(Fmoc). Maldi-Tof on the crudeproduct: 6000 (calc. 6000) showing only minor impurities.

Example 2. Preparation of the Thio-Guanine Monomer

1. 6-Chloroguanine (4.93 g) and 10.05 g K₂CO₃ was stirred with 40 mL DMFfor 10 minutes at room temperature. The reaction mixture was placed in awater bath at room temperature and 3.55 mL ethyl bromoacetate was added.The mixture was stirred in a water bath until TLC (20% Methanol/DCM)showed that the reaction was finished. The precipitated carbonate wasfiltered off and washed twice with 10 mL DMF. The solution, which was alittle cloudy, was added to 300 ml water, whereby it became clear. On anice bath the target compound slowly precipitated. After filtration thecrystals were washed with cold ethanol and dried in a desiccator. Theyield for this step was 3.3 g (44.3%) of ethyl chloroguanine acetate.

2. Ethyl chloroguanine acetate (3.3 g) was dissolved by reflux in 50 mLabsolute ethanol. Thiourea (1.08 g) was added. After a refluxing for ashort time, precipitate slowly began forming. According to TLC (20%Methanol/DCM) the reaction was finished in 45 minutes. Upon completion,the mixture was cooled on an ice bath. The precipitate was then filteredand dried overnight in a desiccator. The yield for this step was 2.0 g(60%) ethyl thioguanine acetate.

3. Ethyl thioguanine acetate (3.57 g) was dissolved in 42 mL DMF.Benzylbromide (2.46 mL) was then added and the mixture stirred in an oilbath at 45° C. The reaction was followed using TLC (25% Methanol/DCM).After 3 hours all basis material was consumed. The step 3 targetcompound precipitated upon evaporation under reduced pressure and hightemperature. The precipitate was recrystallized in absolute ethanol,filtered and then dried in a desiccator. The yield for this step was3.88 g (82%) of methyl benzyl thioguanine ethylester.

4. Methyl benzyl thioguanine ethylester (5.68 g) was dissolved in 12.4mL of 2 M NaOH and 40 mL THF, and then stirred for 10 minutes. The THFwas evaporated by. This was repeated. The material was dissolved inwater and then 6.2 mL of 4 M HCl was added, whereby the target productprecipitated. Filtering and drying in a desiccator. The yield for thisstep was 4.02 g (77%).

5. The product of step 4 (4.02 g), 3.45 g backbone ethylester, 9 mL DMF,3 mL pyridine, 2.1 mL triethylamine and 7.28 g PyBop were mixed and thenstirred at room temperature. After 90 minutes a solid precipitationformed. The product was taken up in 125 mL DCM and 25 mL methanol. Thissolution was then extracted, first with a mixture of 80 mL of 1MNaCitrate and 20 mL of 4M HCl, and then with 100 mL dilute aqueousNaHCO₃. Evaporation of the organic phase gave a solid material. Thematerial was dissolved in 175 mL boiling ethanol. The volume of thesolution was reduced to about 100 mL by boiling. Upon cooling in an icebath, the target product precipitate. The crystals were filtered, washedwith cold ethanol and then dried in a desiccator. The yield of this stepwas 6.0 g (86%.)

6. The product of step 5 (6.0 g) was dissolved in 80 mL THF, 7.5 mL 2MNaOH and 25 mL water. The solution became clear after ten minutes ofstirring. THF was evaporated. Water (50 mL) was added to the mixture.THF was evaporated. Water (50 mL) was added to the mixture. When the pHwas adjusted by the addition of 3.75 mL of 4M HCl, thio-guanine monomerprecipitated. It was then filtered, washed with water and dried in adesiccator. The yield for this step was 5.15 g (91%).

Example 3. Preparation of Diaminopurine Acetic Acid Ethyl Ester

1. Diaminopurine (10 g) and 40 g of K₂CO₃ were added to 85 mL of DMF andstirred for 30 minutes. The mixture was cooled in a water bath to 15° C.Ethyl bromoacetate (3 mL) was added three times with 20 minute intervalsbetween each addition. This mixture was then stirred for 20 minutes at15° C. The mixture was left in the water bath for another 75 minutes,and the temperature increased to 18° C. The DMF was removed by filteringand the remaining K₂CO₃ was added to 100 mL of ethanol and refluxed for5 minutes. Filtering and repeated reflux of the K₂CO₃ in 50 mL ethanol,filtering. The pooled ethanol phases were placed in a freezer, afterwhich crystals formed. These crystals were filtered, washed with coldethanol, filtered again and then dried in a desiccator overnight. Theyield for this step was 12 g (76%).

Example 4. Preparation of L₃₀-Linker

1. A solution of 146 mL of 2,2′-(Ethylenedioxy)bis(ethylamine) (98%) in360 mL of THF was cooled in an ice bath. Di-tert-butyl dicarbonate (97%)(65 g) in 260 mL THF was added dropwise over one hour. The solvent wasevaporated. The remaining oil was dissolved in water and then evaporatedoff. The oily product was dissolved in 300 mL water, extracted with 300mL DCM, then washed twice with 150 mL of DCM. The collected organicphase was washed with 50 mL of water before evaporating to about halfthe volume. The organic phase was then extracted with 400 mL of 1MNaCitrate (pH 4.5), and then extracted again with 50 mL of 1M NaCitrate(pH 4.5). The aqueous phases were washed with 50 mL DCM before coolingon an ice bath. While stirring, 100 mL of 10M NaOH was added to theaqueous washed aqueous phases resulting in pH of 13-14. In a separationfunnel the product separated on its own. It was shaken with 300 mL DCMand 50 ml water. The organic phase was evaporated, yielding a white oil.The yield for this step was 48.9 g (65.7%). The product had a predictedmolecular formula of C₁₁H₂₄N₂O₄ (MW 248.3).

2. Boc-amine (76.2 g) was dissolved in 155 mL pyridine. Diglycolicanhydride (54.0 g) (90%) was added. After stirring for 15 minutes theintermediate product separated out and then 117 mL Acetic Anhydride(min. 98%) was added and the mixture stirred at 95° C. for 1 hour. Thesolution was then put under reduced pressure and evaporated. Water (117mL) was added, and the mixture was then stirred for 15 minutes, afterwhich 272 mL of water and 193 mL of DCM were added. The organic layerwas extracted twice with 193 mL of 1M Na₂CO₃ and then twice with amixture of 72 mL of 4M HCl and 289 mL of 1M NaCitrate. After eachextraction the aqueous phase was washed with a little DCM. The collectedorganic phase was washed with 150 mL of water. The solvent wasevaporated leaving the product as an orange oil. This yield for thisstep was 100.3 g (0.29 mol) (94%). The product had a predicted molecularformula of C₁₅H₂₆N₂O₇ (MW 346.4).

3. The product from step 2 (100.3 g) was dissolved in an equal amount ofTHF and was then added dropwise to 169.4 mL of2,2′-(Ethylendioxy)bis(ethylamine) at 60° C. over the period of 1 hour.The amine was distilled from the reaction mixture at 75-80° C. and apressure of 3×10⁻¹ mBar. The residue from the distillation was taken upin a mixture of 88 mL of 4M HCl and 350 mL of 1M NaCitrate and thenextracted three times with 175 mL of DCM. The aqueous phase was cooledin an ice bath and was cautiously added to 105 mL of 10M NaOH whilestirring. In a separation funnel the product slowly separated from thesolution. When separated 100 mL of water and 950 mL of DCM were added tothe product. Stirring for some minutes before pouring to a separationfunnel. The pH in the aqueous phase should be 14. The aqueous phase wasextracted four times with 150 mL of DCM. The solvent was evaporated. Theoily residue was dehydrated by evaporation from toluene, giving a yellowoil. The yield for this step was 115.48 g (81%). The product had apredicted molecular formula of C₂₁H₄₂N₄O₉ (MW 494.6).

4. The Boc-amine (115.48 g) from step 3 was dissolved in 115 mL ofpyridine. Diglycolic anhydride (40.6 g) (90%) was added and the mixturestirred for 15 minutes, after which the intermediate product came out.Acetic Anhydride (97 mL) (min. 98%) was added and the mixture stirred at95° C. for 1 hour. The mixture was then evaporated under reducedpressure. The mixture was then cooled and then 80 mL of water was added.This mixture was stirred for 15 minutes and then 200 mL of water and 150mL of DCM were added. The organic layer was extracted twice with 150 mLof 1M Na₂CO₃ and then twice with a mixture of 53 mL of 4M HCl and 213 mLof 1M NaCitrate. After each extraction the aqueous phase was washed witha little DCM. The collected organic phase was washed with 150 mL ofwater. The solvent was evaporated. The oily residue was dehydrated byevaporation from toluene, giving a yellow oil. The yield for this stepwas 125 g (92%). The product had a predicted molecular formula ofC₂₅H₄₄N₄O₁₂ (MW 592.6), with a mass spectrometry determined molecularweight of 492.5.

Further purifying of the product could be done on a silica column with agradient from 5-10% methanol in DCM. The yield from the columnpurification was 69% and produced a white oil.

5. White oil (12.4 g) from step 4 was dissolved in a mixture of 12 mLwater and 12 mL 1,4-Dioxane (99%) and was then heated to reflux. DIPEA(6 mL) was added and refluxed for 30 minutes. This mixture was cooledand then evaporated. The oily residue was dehydrated by evaporation fromtoluene, giving a yellow oil. The product had a predicted molecularformula of C₂₅H₄₆N₄O₁₄ (MW 610.6).

Example 5. Exemplary Embodiments of PNA Sequences

All are made by PNA standard procedures (see Examples 17 and 18).

TABLE 1 SEQUENCE PNA N- C- MOLECULAR DESIGNATION SEQUENCES¹ TERMINALTERMINAL WEIGHT SEQ. AA TCD-DG_(s)G_(s)- FLU-L₃₀- -LYS(CYS) 8805 TAC-ASEQ. AB U_(s)GU_(s)-DPP- FLU-L₃₀- -LYS(CYS) 8727 TTG-D SEQ. ACCU_(s)G_(s)-G_(s)DD- FLU-L₃₀- -LYS(CYS) 9413 TU_(s)D-G_(s)DC SEQ. ADGTP-TAA- FLU-L₃₀- -LYS(CYS) 9203 TTP-PAG SEQ. AE DG_(s)T-CG_(s)D-FLU-L₃₀- -LYS(CYS) 9413 DG_(s)G-U_(s)CU_(s) SEQ. AF AGA-CPT- FLU-L₃₀--LYS(CYS) 9187 TPG-APT SEQ. AG TCD-DII- FLU-L₃₀- -LYS(CYS) 8742 TAC-A¹Flu is fluorescein; T is thiamine; C is cytosine; D is diaminopurine;G_(s) is thioguanine; A is Adenine; U_(s) is 2/4-thiouracil; G isguanine; P is pyrimidone; I is inosine.

Example 6. Three PNAs with the L₃₀ Linker with Different Amino Acids atthe C-terminal

BA: Flu-L₃₀-DGT-DTC-GTD-CCG-Lys(Acetyl) BB:Flu-L₃₀-DGT-DTC-GTD-CCG-Lys(Cys) BC: Flu-L₃₀-DGT-DTC-GTD-CCG-Lys(Lys)₃

Example 7. Synthesis of Flu-L₉₀-Lys(Flu)-L₃₀-Lys(Cys)

Using procedure provided in Example 18a, an MBHA-resin was loaded withBoc-Lys(Dde)-OH. Using a peptide synthesizer, amino acids were coupledaccording to PNA solid phase procedure provided in Example 18d yieldingBoc-L₉₀-Lys(Fmoc)-L₃₀-Lys(Dde). The Boc and Fmoc protections groups wereremoved and the amino groups marked with flourescein using the procedurein Example 18e. Then, the Dde protection group was removed and 0.4 Mcysteine was added according to the procedure in Example 18b. The PNAwas cleaved from the resin, precipitated with ether and purified on HPLCaccording to Example 18d. The product was found to have a molecularweight of 3062 using MALDI-TOF mass spectrometry; the calculatedmolecular weight is 3061.

Example 8. Synthesis of a Conjugate Made from Sequence AA from Example5, DexVS70, and Flu(10)

Dextran (with a molecular weight of 70 kDa) was activated withdivinylsulfone to a degree of 92 reactive groups/dextran polymer; thisproduct is designated DexVS70.

280 μL DexVS70  20 nmol  66 μL Flu₂Cys 160 nmol (prepared from Example7)  25 μL 0.8M NaHCO₃ pH = 9.5  29 μL H₂O

The above four compounds were mixed. The mixture was placed in a waterbath at 30° C. for 16 hours. The mixture was added to 50 nmol offreeze-dried PNA (sequence AA from Example 5). The mixture was placed ina water bath at 30° C. for 30 minutes. The conjugating reaction wasquenched with 50 μL of 500 mM cysteine for 30 minutes at 30° C.Purification of the product was performed using FPLC: columnSUPERDEX®—200, buffer 10 mM Hepes 100 mM NaCl, method 7 bank 2, Loop 1mL. Two fractions were collected: one with the product and one with theresidue. The relative absorbance Flu₂ (ϵ_(500nm)=146000 M⁻¹,ϵ_(260nm)=43350 M⁻¹) and PNA (ϵ_(500nm)=73000 M⁻¹, ϵ_(260nm)=104000 M⁻¹)was used to calculate the average conjugation ratio of Flu₂, PNA, andDexVS70. The conjugation ratio of Flu₂ to DexVS70 was 9.4. Theconjugation ratio of PNA (sequence AA) to DexVS70 was 1.2.

Example 9. Synthesis of HRP-DexVS70-Seq. AA

Using the procedure of Example 14, the conjugate HRP-DexVS70-Seq. AA wasmade. The ratio of HRP to DexVS70 is 12.2; the ratio of Seq. AA to Dex70is 1.2.

Example 10. Synthesis of GaM-DexVS70-Seq. AB

The synthesis of GaM-DexVS70-Seq. AB was performed using the procedurein Example 16 with the following changes as indicated.

Dextran (molecular weight 70 kDa) is activated with divinylsulfone to adegree of 92 reactive groups/dextran polymer.

105.0 μL DexVS70 7.5 nmol  57.0 μL Goat anti mouse Imuno globuline(GAM-Ig)  15 nmol  8.9 μL 4M NaCl  10.6 μL 0.8M NaHCO₃ (pH = 9.5) 144.5μL H₂O

The above five components were mixed and placed in a water bath at 30°C. for 40 minutes. Two hundred and ninety μL were taken out of themixture and added to 100 nmol of Seq. AB, which was previously dissolvedin 80 μL of H₂O. Then, 20 μL of 0.8 M NaHCO₃ (pH 9.5) was added and themixture placed in a water bath at 30° C. for 1 hour. Quenching wasperformed by adding 39 μL of 500 mM cysteine and letting the resultantmixture set for 30 minutes at 30° C.

Purification of the product on FPLC: column SUPERDEX®—200, buffer 10 mMHepes 100 mM NaCl, method 7 bank 2, Loop 1 mL. Two fractions werecollected: one with the product and one with the residue. Relativeabsorbance PNA(Flu) (ϵ_(500nm)=73000 M⁻¹) and GAM (ϵ_(278nm)=213000 M⁻¹)(correction factor for PNA at 278 nm is due to the specific PNA and iscalculated: 278/500 nm) was used to calculate the average conjugationratio of PNA, GAM and DexVS70. The ratio of PNA to DexVS70 was 5.3 andthe ratio of GaM to DexVS70 was 0.8.

Example 11. Exemplary Embodiments of PNA1-DexVS-PNA2 Conjugates

TABLE 2 PNA1 PNA2 Conjugate PNA1 to PNA2 to designation ratio PNA1 nmolDexVS PNA2 nmol DexVS DexVS Conj. CA 1:9 Seq. AA 12.5 1.02 Seq. AD 1008.2 DexVS70 Conj. CB 1:6 Seq. AC 40 1.5 Seq. AB 200 7.4 DexVS70 Conj. CC 1:16 Seq. AC 13.3 0.84 Seq. AB 200 12.7 DexVS150 Conj. CD 1:6 Seq. AC40 2.3 Seq. AB 200 11.5 DexVS150All conjugates were made by standard conjugation procedures of Example17.

Example 12. Synthesis of Anti-Human-BCL2-DexVS70-PNA

Dextran (molecular weight 70 kDa) was activated with divinylsulphone toa degree of 92 reactive groups/dextran polymer, and is designatedDexVS70. The antibody Anti-Human-BCL2 is designated AHB.

105 μL DexVS70  7.5 nmol 800 μL AHB conc. (2.9 g/L) 15.1 nmol  25 μL 4MNaCl  32 μL 0.8M NaHCO₃ (pH = 9.5)

The above four compounds were mixed and placed in a water bath at 30° C.for 65 minutes. From this mixture, 875 μL was taken out and added to theindicated number of nmol of PNA in the table below; before the additionthe PNA had been dissolved in the μL of H₂O indicated in the tablebelow. Then the number of μLs of 0.8 M NaHCO₃ (pH 9.5) was addedaccording to the table below. The resulting mixture was placed in awater bath at 30° C. for 70 minutes. Quenching was performed by adding 6mg of solid cysteine (0.05 M) to the mixture and letting it stand for 30minutes at 30° C.

Purification of the product on FPLC: column SUPERDEX®—200, buffer 10 mMHepes 100 mM NaCl, method 7 bank 2, Loop 1 mL. Two fractions werecollected: one with the product and one with the residue. Relativeabsorbance PNA(Flu) (ϵ_(500nm)=73000 M⁻¹) and AHB (ϵ_(278nm)=213000 M⁻¹)(correction factor for PNA at 278 nm is due to the specific PNA and iscalculated: 278/500 nm) was used to calculate the average conjugationratio of PNA, AHB and DexVS70.

Conjugates with different ratios PNA are shown in the following table.

TABLE 3 nmol of μL of μL of 0.8M Conjugate PNA H₂O NaHCO₃ (pH 9.5) PNAto AHB to designation added added added DexVS70 DexVS70 Conj. DA 100 7525 9.5 1.6 Conj. DB 33 30 10 2.9 1.2 Conj. DC 67 60 20 5.6 1.1

Example 13. Solid Phase Synthesis and Purification of Lys(Flu)-L₃₀-Chr17:14-L₃₀-Lys(Flu)-L₉₀-Lys(Flu)-L₉₀-Lys(Flu)

All Standard procedures are described in Example 18.

1. An MBHA-resin was loaded withBoc-L₃₀-Lys(Fmoc)-L₉₀-Lys(Fmoc)-L₉₀-Lys(Fmoc) using a standard loadingprocedure to a loading of 0.084 mmol/g.

2. To this resin, Boc-Lys(Fmoc)-L₃₀-AAC-GGG-ATA-ACT-GCA-CCT- was coupledusing the peptide synthesizer machine following standard PNA solid phasechemistry. Fmoc protection groups were removed and the amino groups werelabeled with fluorescein. After cleaving and precipitation the PNA wasdissolved in TFA. The precipitate was washed with ether. The precipitatewas dissolved in 200 μL NMP To this solution 6 mg Fmoc-Osu was added anddissolved. Next, DIPEA (9 μL) was added and the reaction was followedusing MALDI-TOF mass spectrometry. After 30 minutes the reaction wasfinished and the PNA was precipitated and washed with ether.

HPLC after dissolving the PNA in 30% CH₃CN and 10% TFA/H₂O gave threepure fractions. The fractions were pooled and lyophilized. Thelyophilized PNA was then dissolved in 192 μL NMP. Piperidine (4 μL) and4 μL DBU was added to this solution which set for 30 minutes. Analysisby MALDI-TOF mass spectrometry gave a molecular weight of 10777.

The precipitate was washed with ether and was then dissolved in 100 μLTFA. The precipitate was washed with ether and then dried using N₂ gas.

Example 14. Standard Synthesis of HRP-DexVS70-PNA Conjugate

Dextran (molecular weight 70 kDa) is activated with divinylsulfone to adegree of 92 reactive groups/dextran polymer.

192 μL DexVS70 13.7 nmol 255 μL horse radish peroxidase (HRP)  602 nmol 15 μL 4M NaCl  19 μL 0.8M NaHCO₃ pH = 9.5 119 μL H₂O

The above five components are mixed together placed in a water bath at30° C. for 16 hours. Five hundred microliters of this mixture are addedto 50 nmol PNA, which is previously dissolved in 40 μL H₂O. Then, 10 μLof 0.8 M NaHCO₃ (pH 9.5) is added. The mixture is then placed in a waterbath at 30° C. for 2 hours. Quenching is performed by adding 55 μL of110 mM cysteine and letting the resultant mixture set for 30 minutes at30° C.

Purification of the product is performed by FPLC: column SUPERDEX®—200,buffer 10 mM Hepes 100 mM NaCl, method 7 bank 2, Loop 1 mL.

Two fractions are collected: one with the product and one with theresidue. Relative absorbance HRP (ϵ_(404nm)=83000 M⁻¹, ϵ_(500nm)=9630M⁻¹) and PNA(Flu) (ϵ_(500nm)=73000 M⁻¹) is used to calculate the averageconjugation ratio of HRP, PNA and DexVS70.

Example 15. Standard Synthesis of GAM-DexVS70-PNA Conjugate

Dextran (molecular weight 70 kDa) is activated with divinylsulfone to adegree of 92 reactive groups/dextran polymer (DexVS70).

105.0 μL DexVS70 7.5 nmol  57.0 μL Goat anti mouse Imuno globuline (GAM) 15 nmol  8.9 μL 4M NaCl  10.6 μL 0.8M NaHCO₃ (pH = 9.5) 144.5 μL H₂O

The above five components are mixed and placed in a water bath at 30° C.for 40 minutes. Two hundred and ninety μL is taken out of the mixtureand added to 50 nmol of PNA, which is previously dissolved in 40 μL ofH₂O. Then, 10 μL of 0.8 M NaHCO₃ (pH 9.5) is added and the mixtureplaced in a water bath at 30° C. for 1 hour. Quenching is performed byadding 34 μL of 500 mM cysteine and letting the resultant mixture setfor 30 minutes at 30° C.

Purification of the product on FPLC: column SUPERDEX®—200, buffer 10 mMHepes 100 mM NaCl, method 7 bank 2, Loop 1 mL. Two fractions arecollected: one with the product and one with the residue. Relativeabsorbance PNA(Flu) (ϵ_(500nm)=73000 M⁻¹) and GAM (ϵ_(278nm)=213000 M⁻¹)(correction factor for PNA at 278 nm is due to the specific PNA and iscalculated: 278/500 nm) was used to calculate the average conjugationratio of PNA, GAM and DexVS70.

Example 16. Standard Synthesis of PNA1-DexVS70-PNA2

Dextran (molecular weight 70 kDa) is activated with divinylsulfone to adegree of 92 reactive groups/dextran polymer. PNA1 (100 nmol) isdissolved in 140 μL of DexVS70 (10 nmol). To this mixture 12.5 μL ofPNA2 (12.5 nmol) dissolved in H₂O is added, and then 30 μL of NaHCO₃ (pH9.5) is added and the solution mixed. The resultant mixture is placed ina water bath at 30° C. for 35 minutes. Quenching was performed by adding18.3 μL of 500 mM cysteine in Hepes and letting this mixture set for 30minutes at 30° C.

Purification of the product on FPLC: column SUPERDEX®—200, buffer 10 mMHepes 100 mM NaCl, method 7 bank 2, Loop 1 mL. Two fractions arecollected: one with the product and one with the residue. Relativeabsorbance PNA(Flu) (ϵ_(500nm)=73000 M⁻¹) and the proportion between thetwo PNA's is used to calculate the average conjugation ratio of PNA, PNAand DexVS70.

Example 17. Synthesis of the Boc-PNA-I(O-Bz)-Monomer

6-Benzyloxypurine. Sodium hydride (60% Dispersion in mineral oil; 3.23g; 80 mmol) was slowly added to benzyl alcohol (30 ml; 34.7 mmol). Afterthe addition of more benzyl alcohol (10 ml) and 6-chloropurine (5.36g;). The reaction mixture was heated to 100° C. for 4 hours. When thereaction mixture has reached room temperature, water (1 ml) was slowlyadded. 6-Benzyloxypurine was precipitated by the addition of acetic acid(4.6 ml) and diethylether (550 ml). The precipitate was separated byfiltration (11.72 g). Re-crystallization from ether gave (4.78 g;65.4%). Melting point was 175-177° C. (litt. 170-172° C.)[Ramazaeva N.,1989 #473] 1H-NMR (DMSO-d6): 8.53 (1H, s); 8.39 (1H, s); 7.54-7.35 (5H,m); 5.62 (2H, s).

Methyl (6-(Benzyloxy)purin-9-yl) acetate

6-Benzyloxypurine (4.18 g; 18.5 mmol) was added to a suspension ofpotassium carbonate (3.1 g; 22.4 mmol) in DMF (100 ml). After 15 min.,bromoacetic acid methyl ester (1.93 ml; 20.4 mmol) was added. Thereaction was monitored by TLC in butanol:acetic acid:water 4:1:1. Uponcompletion, the reaction mixture was partitioned between water (600 ml)and ethyl acetate (600 ml). The organic phase was dried over magnesiumsulfate and evaporated to a volume of ˜10 ml and precipitated with pet.ether. The two products were separated by column chromatography usingethyl acetate as the solvent. The products were precipitated in pet.ether. Yield: 2.36 g (43%). Melting point: 111.5-115° C. UV λmax=250 nm(9-alkylated); λmax=260 nm (7-alkylated). 1H-NMR (DMSO-d6): 8.60 (1H,s); 8.43 (1H, s); 7.6-7.35 (5H, m); 5.69 (2H, s); 5.26 (2H, s); 3.75(3H, s).

(6-(Benzyloxy)purin-9-yl) acetic acid

Methyl (6-(Benzyloxy)purin-9-yl) acetate (2.10 g; 7.0 mmol) wasdissolved in methanol (70 ml) and 0.1 M NaOH (85 ml) is added. After 15min. the pH of the reaction mixture was lowered by addition of 0.1 M HCl(˜80 ml) to pH 3. The precipitate was separated from the mixture byfiltration and washed with water and ether. Yield: 1.80 g (90.2%).1H-NMR (DMSO-d6): 8.55 (1H, s); 8.37 (1H, s); 7.55-7.30 (5H, m); 5.64(2H, s); 5.09 (2H, s).

N-((6-(Benzyloxy)purin-9-yl) acetyl)-N-(2-Boc-aminoethyl)glycine

Ethyl N-(2-Boc-aminoethyl)glycinate (0,285 g; 1.15 mmol),(6-(benzyloxy)purin-9-yl) acetic acid (0,284 g; 1.0 mmol) and3-hydroxy-1,2,3 benzotriazin-4(3H)-one (0.180; 1.1 mmol) was dissolvedin dichlormethane/dimethylformamide 1:1 (10 ml). After addition ofdicycloehexylcarbodiimide (0,248 g; 1.2 mmol) the reaction was left overnight. The precipitate was removed by filtration. The organic phase wasextracted twice with saturated sodium bicarbonate, dried with magnesiumsulfate and evaporated to a oil. Column purification on silica usingdichloromethane with 0-5% methanol as elutant yields the monomer esterwhich was dissolved in methanol (10 ml). Then, 0.1 M NaOH (12 ml) wasadded. After 30 min the reaction was filtered and pH adjusted withsaturated KHSO4/water (1:3) to 2,7. The water phase was extracted twicewith ethyl acetate (2×100 ml). The combined organic phases were driedover magnesium sulfate and evaporated to a volume of 10 ml.Precipitation with pet. ether yielded the monomer (0.15 g; 31%). 1H-NMR(DMSO-d6): 8.51 (1H, s); 8.23 (1H, s); 7.6-7.3 (5H, m); 5.64 (2H, s);5.31 (ma.)+5.13 (mi.) (2H, s); 4.23 (mi.)+3.98 (ma.) (2H, s); 3.55-3.00(4H, m); 1.36 (9H, s).

The synthesis of the hypoxanthine PNA monomer. (i) BnOH, NaH (ii) K2CO3,BrCH2CO2CH3 (iii) OH— (iv) DCC, Dhbt-OH, Boc-aeg-OEt (v) OH—

The Boc-PNA-Diaminopurine-(N6-Z)-monomer was prepared according toGerald Haaima, Henrik F. Hansen, Leif Christensen, Otto Dahl and PeterE. Nielsen; Nucleic Acids Research, 1997, Vol 25, Issue 22 4639-4643.

The Boc-PNA-2-Thiouracil-(S-4-MeOBz)-monomer was prepared according toJesper Lohse, Otto Dahl and Peter E. Nielsen; Proceedings of theNational Academy of Science of the United States of America, 1999, Vol96, Issue 21, 11804-11808.

The Boc-PNA-Adenine-(Z)-monomer was from PE Biosystems catalogGEN063011.

The Boc-PNA-Cytosine-(Z)-monomer was from PE Biosystems cat. GEN063013.

The Boc-PNA-Guanine-(Z)-monomer was from PE Biosystems cat. GEN063012.

The Boc-PNA-Thymine-monomer was from PE Biosystems cat. GEN063010.

IsoAdenine (2-aminopurine) may be prepared as a PNA-monomer by 9-Nalkylation with methylbromoacetate, protection of the amino group withbenzylchloroformate, hydrolysis of the methyl ester, carbodiimidemediate coupling to methyl-(2-Boc-aminoethyl)-glycinate, and finallyhydrolysis of the methyl ester.

4-thiouracil may be prepared as a PNA-monomer by S-protection with4-methoxy-benzyl chloride, 1-N alkylation with methylbromoacetate,hydrolysis of the methyl ester, carbodiimide mediate coupling tomethyl-(2-Boc-aminoethyl)-glycinate, and finally hydrolysis of themethyl ester.

Thiocytosine may be prepared as a PNA monomer by treating theBoc-PNA-cytosine(Z)-monomer methyl ester with Lawessons reagent,followed by hydrolysis of the methyl ester.

A number of halogenated bases are commercially available, and may beconverted to PNA monomers analogously to the non-halogenated bases.These include the guanine analog 8-bromo-guanine, the adenine analogs8-bromo-adenine and 2-fluoro-adenine, the isoadenine analog2-amino-6-chloro-purine, the 4-thiouracil analog 5-fluoro-4-thio-uracil,and the 2-thiouracil analog 5-chloro-2-thiouracil.

Boc-PNA-Uracil monomers were first described in “Uracil og 5-bromouracilI PNA,” a bachelor project by Kristine Kilså Jensen, KøbenhavnsUniversitet 1992.

Example 18. Miscellaneous Standard Procedures

a. Loading of Resins.

P-methyl-BHA-resin (3 g) is loaded with Boc-Lys(Fmoc)-OH 15 mmol/gresin. The lysine is dissolved in NMP and activated with 0.95equivalents (eq.) HATU and 2 eq. DIPEA. After loading the resin, it iscapped by adding a solution of (Ac)₂O/NMP/pyridine (at a ratio of 1/2/2)and letting it set for at least 1 hour or until Kaiser test wasnegative. After washing with DCM, the resin is dried in a dessicator.Quantitative Kaiser test typically gives a loading of 0.084 mmol/g.

b. Amino Acid Couplings.

The Boc protection group is removed from the resin with TFA/m-cresol (ata ratio of 95/5) 2×5 min. The resin is then washed with DCM, pyridineand DMF before coupling with the amino acid, which is dissolved in NMPin a concentration between 0.2 and 0.4 M and activated with 0.95 eq. ofHATU and 2 eq of DIPEA for 2 minutes. The coupling is complete when theKaiser test is negative. Capping occurring by exposing the resin for 3minutes to (Ac)₂O/pyridine/NMP (at a ratio of 1/2/2). The resin is thenwashed with DMF and DCM

c. Boc-L₃₀₀-Lys(Fmoc)-Resin.

To the loaded Boc-Lys(Fmoc)-resin, L₃₀-Linker in a concentration of 0.26M was coupled using standard amino acid coupling procedure. This wasdone 10 times giving Boc-L₃₀₀-Lys(Fmoc)-resin.

d. PNA Solid Phase.

On a peptide synthesizer (ABI 433A, Applied Biosystems) PNA monomers arecoupled to the resin using standard procedures for amino acid couplingand standard PNA chemistry. Then the resin is handled in a glass vial toremove protections groups and to label with either other amino acids orflourophores.

Removal of the indicated protection groups is achieved with thefollowing conditions:

Boc: TFA/m-cresol (at a ratio of 95/5) 2×5 min.

Fmoc: 20% piperidine in DMF 2×5 min.

Dde: 3% hydrazine in DMF 2×5 min.

When the synthesis is finished, the PNA is cleaved from the resin withTFA/TFMSA/m-cresol/thioanisol (at a ratio of 6/2/1/1). The PNA is thenprecipitated with ether and purified on HPLC. MALDI-TOF massspectrometry is used to determine the molecular weight of the product.

e. Labeling with Fluorescein.

5(6)-carboxy fluorescein is dissolved in NMP to a concentration of 0.2M. Activation is performed with 0.9 eq. HATU and 1 eq. DIPEA for 2 minbefore coupling for at least 2×20 min or until the Kaiser test isnegative.

Example 19. PNA with Positive and Negative Loadings

In order to make better conjugations at one time we tried to give thePNA a loading. Both PNA's were made by PNA standard procedures (SeeExample 18).

1. Flu-L₃₀-Glu-TCA-AGG-TAC-A-Glu-L₃₀₀-Lys(Cys)

Glu=glutamate has negative loadings and for the easiness the PNA isdesignated -A4

2. Flu-L₃₀-Lys(Me)₂-TGT-ACC-TTG-A-Lys(Me)₂-L₃₃₀- Lys(cys)

Lys(Me)₂=Boc-Lys(Me)₂-OH has positive loadings and the PNA isdesignated+T+

TABLE 4 HRP/ GaM/ PNA/ name number HRP GaM equiv. Dex Dex Dex −A4−D13041 D13050 9 12.3 0.13 −A4− D13041 D13060 7 0.94 0.66 +T4+ D13042D13058 9 13.5 0.19 +T4+ D13042 D13056 7 1.42 0.45As it is shown in the scheme, PNAs with loading are not good atcoupling.

Example 20. Target Detection: Procedures Used in the Examples Below

1. Fixation of Biological Samples

Tonsil tissue samples were fixed in neutral buffered formalin, NBF (10mM NaH₂PO₄/Na₂HPO₄, pH 7.0), 145 mM NaCl, and 4% formaldehyde (allobtained from Merck, Whitehouse Station, N.J.). The samples wereincubated overnight in a ventilated laboratory hood at room temperature.

2. Sample Dehydration and Paraffin Embedding

The tissue samples were placed in a marked plastic histocapsule (Sakura,Japan). Dehydration was performed by sequential incubation in 70%ethanol twice for 45 min, 96% ethanol twice for 45 min, 99% ethanoltwice for 45 min, and xylene twice for 45 min. The samples weresubsequently transferred to melted paraffin (melting point 56-58° C.)(Merck, Whitehouse Station, N.J.) and incubated overnight (12-16 hours)at 60° C. The paraffin-infiltrated samples were transferred to freshwarm paraffin and incubated for an additional 60 min prior to paraffinembedding in a cast (Sekura, Japan). The samples were cooled to form thefinal paraffin blocks. The marked paraffin blocks containing theembedded tissue samples were stored at room temperature in the dark.

3. Cutting, Mounting and Deparaffination of Embedded Samples

The paraffin blocks were cut and optionally also mounted in a microtome(0355 model RM2065, Feather S35 knives, set at 5.0 micrometer; Leica,Bannockburn, Ill.). The first few millimeters were cut and discarded.Paraffin sections 4-6 micrometers thick were then cut and collected atroom temperature. The sections were gently stretched on a 45-60° C. hotwater bath before being mounted onto marked microscope glass slides(SUPERFROST® Plus; Fisher, Medford, Mass.), two tissue sections perslide. The slides were then dried and baked in an oven at 60° C. Theslides were deparaffinated by incubating twice in xylene for 5 min±2 mintwice, then in 96% ethanol for 2 min +/−30 sec, then twice in 70%ethanol for 2 min +/−30 sec, and then once in Tris-buffered saline withTWEEN® (called herein TBST) for 5 min. TBST comprises 50 mM Trisadjusted to pH 7.6 with HCl; 150 mM NaCl; 0.05% TWEEN®20. The slideswere deparaffinated by subsequently incubation in xylene twice for 5min±2 min, 96% ethanol twice for 2 min +/−30 sec and 70% ethanol twicefor 2 min +/−30 sec. The slides were immersed in deionized water andleft for 1 to 5 min.

4. Endogenous Peroxidase Blocking

Samples were incubated with a 3% hydrogen peroxide solution for 5 min.to quench endogenous peroxidase activity, followed by washing indeionized water for 1 to 5 min.

5. Antigen Retrieval by Microwave Oven

Antigens in the sample were retrieved by immersing the slides in acontainer containing Antigen Retrieval Solution, pH 6.0 (DakoCytomationcode No. K5204 Vial 7 or optional code No. K5205 Vial 7). The containerwas closed with a perforated lid and placed in the middle of a microwaveoven and left boiling for 10 min. The container was removed from theoven and allowed to cool at room temperature for 20 min. The sampleswere rinsed in deionized water.

6. Antigen Retrieval by Water Bath Incubation

Antigens in the sample were retrieved by immersing the slides in abeaker containing Antigen Retrieval Solution, pH 6.0 (DakoCytomationcode No. K5204 Vial 7 or optional code No. K5205 Vial 7). The sampleswere incubated for 40 min in a water bath at 95-100° C. The beaker wasremoved from the water bath and allowed to cool at room temperature for20 min. The samples were rinsed in deionized water.

7. Water-Repellent Barrier to Liquids by DakoCytomation Pen

To ensure good coverage of reagent on the tissue sample, the area on theslide with tissue was encircled with a silicone rubber barrier usingDakoCytomation Pen (DakoCytomation code No. 2002). The slides weretransferred to a rack and placed in a beaker containing Tris-bufferedsaline with TWEEN® (called herein TBST) and left for 5 min. TBSTcomprises 50 mM Tris adjusted to pH 7.6 with HCl; 150 mM NaCl; 0.05%TWEEN®20.

8. Application of a Primary Antibody

Monoclonal Mouse anti-Human Cytokeratin (DakoCytomation code No. M3515)diluted 1:900 in ChemMate™ Antibody Diluent (DakoCytomation code No.S2022) was applied on the tissue samples and incubated for 30 min in ahumid chamber at ambient temperature. The slides were individuallyrinsed and then washed in TBST for 5 min.

9. Application of Three Primary Antibodies

Monoclonal Mouse Anti-Human Cytokeratin (DakoCytomation code No. M3515)diluted 1:300, 1:900 and 1:1600; monoclonal Mouse Anti-Human CD20cy(DakoCytomation code No. M0755) diluted 1:2000, 1:8000 and 1:14000; andmonoclonal Mouse Anti-Human Ki-67 Antigen (DakoCytomation code No.M7240) diluted 1:400, 1:1200 and 1:2400 were used. The antibodies werediluted in ChemMate™ Antibody Diluent (DakoCytomation code No. S2022),applied on the tissue samples, and incubated for 30 min in a humidchamber at ambient temperature. The slides were individually rinsed andwashed in TBST for 5 min.

10. Application of an Antibody/Dextran/PNA1 Conjugate Recognition Unit

Antibody/Dextran/PNA1 conjugate recognition unit is also called “PNA1conjugate” in the examples that follow. The PNA1 conjugate comprises70,000 molecular weight dextran. Table 5 summarizes PNA1 conjugatesbased on a secondary antibody: goat anti-mouse Ig, called herein GAM(DakoCytomation code No. Z0420). Table 6 summarizes PNA1 conjugatesbased on a primary antibody: mouse anti-human BCL2 oncoprotein, such asClone 124 (DakoCytomation code No. M0887). The primary antibody wasprotein A-purified prior to conjugation. The conjugates were diluted inBBA (50 mM Tris adjusted to pH 7.6 with HCl; 150 mM NaCl; 2% BSA; 0.02%bronidox; 2.44 mM 4-aminoantipyrin) and were applied on the tissuesample in a range of dilutions, then incubated for 30 min in a humidchamber at ambient temperature. The slides were individually rinsed andwashed in TBST for 5 min.

TABLE 5 PNA1 conjugates useful in indirect  recognition of targets: GAM/Dextran/PNA1 Conjugate μM GAM/ PNA1/ No. Sequence Dex Dex Dex D14120AGA CPT TPG DPT 1.25 1.1 4.3 D14102 GTP TAA TTP PAG 1.02 1.0 9.1 D14096GTP TAD TTP PAG 1.15 1.4 4.2 D14083 U_(s)GU_(s) DPP TTG D 0.87 0.8 5.3D13171 U_(s)GU_(s) DPP TTG D 1.21 1.0 7.5 D13161 TTG APP TTA G 2.11 1.16.0 D13150 TGT APP TTGA 2.20 1.1 4.2 D13102 TGT ACC TTGA 2.53 1.1 2.5D12102 TGT ACC TTGA 2.50 1.3 4.5

TABLE 6 PNA1 conjugates for direct recognition of targets: anti-BCL2/Dextran/PNA1 Conjugate μM Ab/ PNA1/ No. SequenceDex Dex Dex D14128 U_(s)GU_(s) DPP TTG D 0.8 1.1 5.6 D14126U_(s)GU_(s) DPP TTG D 1.0 1.2 2.9 D14122 U_(s)GU_(s) DPP TTG D 1.1 1.69.5

In the above tables, the letters A, C, G, U, and T, stand for thenatural bases adenine, cytosine, guanine, uracil, and thymine. P standsfor pyrimidinone, D for 2,6-diaminopurine, and U_(s) for 2-thiouracil.

11. Fixation of PNA1-Conjugate with 1% Glutardialdehyde

The samples were washed in deionized water for 30 sec. Then, 1%glutardialdehyde (Merck Art. No. 820603), called herein GA, diluted in22 mM calcium phosphate buffer, pH 7.2, was applied, and the sampleswere incubated for 10 min in a humid chamber at ambient temperature. Thesamples were washed in deionized water for 30 sec and in TBST for 5 min.

12. Application of a PNA¹-PNA²/Dextran Conjugate Adaptor Unit

PNA¹-PNA²/Dextran conjugate is also called “PNA¹-PNA²” in the followingexamples. Table 7 summarizes the compositions of PNA¹-PNA² conjugates.PNA¹ is complementary to the PNA1 conjugate, and PNA² is complementaryto the PNA2 conjugates D14079 and D13155 described in step 13 below. Thesequence of PNA¹ is CU_(s)G_(s) G_(s)DD TU_(s)D G_(s)DC and the sequenceof PNA² is U_(s)GU_(s) DPP TTG D, in which U_(s) stands for2-thio-uracil, G_(s) stands for 2-amino-6-thioxopurine, D stands fordiaminopurine, and P stands for pyrimidinone. The conjugates, diluted inBBA, were applied to the tissue samples in a range of dilutions, and thesamples were then incubated for 30 min in a humid chamber at ambienttemperature. The samples were individually rinsed and washed in TBST for5 min. When testing a PNA¹-PNA² conjugate, fixed concentrations of 0.08μM PNA1 and 0.05 μM PNA2 were used.

TABLE 7 PNA¹-PNA²/Dextran conjugates Molecular Conjugate weight No. ofdextran PNA¹/dex PNA²/dex μM PNA¹ D14119 150.000 2.3 11.5 4.2 D14106150.000 0.8 12.7 1.3 D14104 70.000 1.5 7.5 3.913. Application of Horse Radish Peroxidase/Dextran/PNA2 ConjugateDetection Unit

Horse Radish Peroxidase (HRP)/Dextran/PNA2 conjugates are also called“PNA2 conjugate” in the examples that follow, and are listed in table 8.The PNA2 conjugates comprise 70.000 Da molecular weight dextran. Theconjugates diluted in BBA were applied to the tissue samples in a rangeof dilutions, and samples were incubated for 30 min in a humid chamberat ambient temperature. The samples were individually rinsed and washedtwice in TBST for 5 min.

TABLE 8 PNA2 conjugates: HRP/Dextran/PNA2 Conjugate μM HRP/ PNA2/ No.Sequence PNA Dex Dex D14133 TCD DII TAC A 1.6 14.0 1.0 D14114DG_(s)T CG_(s)D DG_(s)G U_(s)CU_(s) 3.9 11.4 2.1 D14110DGT CG_(s)D DG_(s)G U_(s)CU_(s) 3.0 12.6 1.6 D14089CU_(s)G_(s) G_(s)DD TU_(s)D G_(s)DC 2.1 14.1 1.5 D14086U_(s)CG_(s) G_(s)DD TU_(s)D GDC 1.9 11.0 1.0 D14079TCD DG_(s)G_(s) TAC A 1.9 12.2 1.2 D13159 CTA AG_(s)G_(s) TCA A 1.9 12.91.3 D13155 TCD DG_(s)G_(s) TAC A 2.4 12.7 1.6 D13148TCA AG_(s)G_(s) TAC A 1.9 11.6 0.8 D13122 CTA AGG TCA A 3.2 13.0 2.1D13108 GTG TGT GT 4.3 12.0 2.3 D13106 TCA AGG TAC A 2.6 12.4 1.3 D12120TCD DGG TAC A 1.0 18.3 0.6 D12094 TCA AGG TAC A 3.0 14.6 0.9In table 8, in addition to the nucleobase letter schemes provided forTables 5-7, I stands for inosine.14. Application of Diaminobenzidine Chromogenic Substrate Solution

The diaminobenzidine chromogenic substrate solution, DAB+(DakoCytomationcode No. K3468) was applied on the tissue samples, and the samples wereincubated for 10 min in a humid chamber at ambient temperature. Thesamples were washed with deionized water for 5 min.

15. Counterstaining with Hematoxylin

The tissue samples were immersed in Mayers Hematoxylin (Bie & BerntsenCode No. LAB00254) for 3 min, rinsed in tap water for 5 min, and finallyrinsed with deionized water.

16. Cover Slipping

Cover slips were applied to the tissue samples using the aqueousmounting media, Faramount (DakoCytomation code No. S3025).

17. Evaluation of the Performance

The tissue staining was examined in a bright field microscope at 10×,20× or 40× magnification. Both the specific and the non-specificstaining intensity were described with a score-system using the range 0to 3+ with 0.5+ score interval. ChemMate™ EnVision™ Detection kitRabbit/Mouse (DakoCytomation code No. K5007 bottle A) was used as areference, and was included in all experiments for testing in parallelwith the PNA conjugates. K5007 was used according to manufacturer'sinstructions. The antibodies were used in the following dilutions: M3515at 1:900, M0755 at 1:8000, and M7240 at 1:1200. The staining intensityof the K5007 reference using the primary antibody M3515 diluted 1:900was set to 2+ in order to compare and assess the staining result of thePNA conjugate tested. If the reference deviated more than ±0.5, the testwas repeated.

In the examples, the various visualization system combinations of theinvention were tested on routine tissue samples. The stainingperformance was compared with a reference visualization system, usingEnVision™ and a very dilute antibody from DakoCytomation. The practicaldynamic range of quantitative IHC may be narrow, and e.g. stronglystained (+3) tissues are not easy to compare with respect to intensity.Therefore, on purpose, the staining intensity of the reference systemwas adjusted to be approximately +2. This was done in order to bettermonitor and compare differences in staining intensity with the system ofthe invention.

Example 21. Protocol for Fast Evaluation of Non-Specific Binding of PNA2Conjugates

The protocol allowed for a quick test of PNA2 conjugates fornon-specific staining. Tonsil tissues were taken through the steps 1-5,7, 13-14, 15 (in which the slides were immersed in a bath of HematoxylinMayer for 1 min.), and 16-17, above. The conjugates to be tested werediluted to the final concentrations 0.05 μM and 0.2 μM. As references,two PNA2 conjugates were used in the final concentration 0.05 μM. Thefirst reference, for example, PNA2, D13108, was known to givenon-specific nuclear staining, and so was used as a positive control.The second reference, for example, PNA2, D13155, was known not to giveany non-specific nuclear staining, and was used as a negative control.In general, 250 μL of each reagent was applied unless otherwisespecified.

Protocol for Test of a PNA Pair with One Antibody.

Tonsil tissues were taken through the steps 1-4, 6-8, 10, 11, and 13-17above. Step 11 was left out for the tonsils not fixed with 1% GA. Ingeneral, 250 μL of each reagent was applied unless otherwise specified.

Protocol for Test of 3-Layer PNA Conjugates

Tonsil tissues were taken through the steps 1-4, 6-8, and 10-17 above.Step 11 was left out for the tonsils not fixed with 1% GA. In general,250 μL of each reagent was applied unless otherwise specified.

Protocol for Test of a PNA Pair with 3 Antibodies

Tonsil tissues were taken through the steps 1-4, 6, 7, 9-11, and 13-17above. Step 11 was left out for the tonsils not fixed with 1% GA. Afurther negative control, mouse IgG1 (DakoCytomation code No. X0931)diluted 1:300 in S2022 was included the protocol for the PNA conjugates.In general, 250 μL of each reagent was applied unless otherwisespecified.

Example 22. Testing and Selection of PNA Pairs

Conjugates comprising example PNA segments were tested for their abilityto specifically hybridize according to the invention. Tonsil tissueswere taken through the steps 1-4, 6-8, 10 and 13-17 above. K5007 wasincluded as a reference to secure the level of the staining. Theconcentration of the conjugates was 0.08 μM for PNA1 and 0.05 μM forPNA2.

The results listed in Tables 9 and 10 show the staining intensities fora representative number of PNA pairs tested. The PNA pairs did notdemonstrate any non-specific binding. The specific staining, in general,was directly proportional to the number of hydrogen bonds involved inthe base-pairing. It was important that each PNA did not interact withitself. Substitution of T (thymine) with U_(s) (2-thiouracil) in somePNAs could prevent such intra-PNA interactions. The unspecific stainingintensity was increased by substituting an A with a D. On the otherhand, we also observed that replacement of one G (guanine) with G_(s)(2-amino-6-thioxopurine) in the same PNA could circumvent the unspecificbinding introduced by D. For instance, the staining of the PNA1conjugate D14102 was improved by substituting the D in D14096 with an Ain D14102. As is apparent from Table 9, this small change resulted in anincrease of the specific staining score by 1+.

TABLE 9 Specific Non-specific PNA1 PNA2 staining intensity stainingintensity D13161 D13159 2 0 D14083 D14079 2.5 0 D14096 D14089 1.5 0D14102 D14089 2.5 0 D14120 D14114 1.5 0

Example 23. The Effect of Base Substitution on PNA-Specific BindingIntensities

The PNA pair D13102-D13106 was used as a starting point for furtherinvestigation of introducing base substitutions in either PNA1 or PNA2conjugates. Tonsil tissues were taken through the steps 1-4, 6-8, 10 and13-17. Each of the three different PNA1 conjugates was tested with eachof the three different PNA2 conjugates. The concentration of theconjugates used was 0.08 μM for PNA1 and 0.05 μM for PNA2.

TABLE 10 PNA2: D13106 D13148 D13155 TCA AGG  TCA AG_(s)G_(s) TCD DG_(s)G_(s)  PNA1: TAC A TAC A TAC A D13102 2.5 0 2 TGT ACC  TTG AD13150 2.5 0.5 3 TGT APP  TTG A D13171 3 2.5 3 U_(s)GU_(s)  DPP TTG D

Table 10 shows the effect of base substitutions on the specific bindingbetween paired PNA variants. No non-specific binding was observed.D13102 tested with D13106 gave a specific staining of 2.5+. Replacementof 2 G's with 2 G_(s)'s (D13148) resulted in the abolishment of specificstaining, but by introducing 2 D's instead of 2 A's (D13155) achieved aspecific staining of 2+. When the 2 C's in D13102 were replaced with 2P's (D13150) and tested with D13106, the specific staining was unchangedat 2.5+, despite the lower number of hydrogen bonds as compared to thePNA-pair D13102-D13106. Test of D13150 with D13148 resulted in a reducedspecific staining of 0.5+, whereas specific staining to 3+ was observedfor the D13150-D13155 pair. The replacement in D13150 of 2 A's with 2D's and of 2 T's with 2 U_(s)'s (D13171) resulted in improved specificbinding compared to D13106. This modified PNA1 was now able to bindspecifically to D13148 with a score of 2.5+, and also bound to D13155.

This experiment clearly demonstrates the use of PNA pairs in the presentinvention. Furthermore, it shows the ability of fine tuning the specificbinding by introducing base substitutions using either natural as wellas non-natural bases.

Example 24. Test of Cross Reactivity

The two PNA-pairs, D13150-D13155 and D13161-D13159, were tested forcross-reactivity. Tonsil tissues were taken through the steps 1-4, 6-8,10, and 13-17. The concentration of conjugates used was 0.16 μM for PNA1and 0.1 μM for PNA2.

As apparent from Table 11, PNA1 D13150 did not cross react with PNA2D13159, but PNA1 D13161 cross reacted with PNA2 D13155. We thereforeexcluded the PNA pair D13161-D13159 due to the cross-reaction betweenD13161 and D13155. No non-specific staining was observed.

TABLE 11 Test of specific binding and cross reactivity PNA2: PNA1:D13155 D13159 D13150 2.0 0 D13161 1 1.5

Example 25. Test of Cross Reactivity

Three PNA-pairs, D14083-D14079, D14102-D14089 and D14120-D14114 weretested for cross-reactivity. Tonsil tissues were taken through the steps1-4, 6-8, 10, and 13-17. The concentration of the conjugates used was0.08 μM for PNA1 and 0.05 μM for PNA2.

The PNA conjugates listed in Table 12 only bound to their complementarypartner and did not cross react to any of the other PNA conjugatestested. No non-specific staining was observed. See Table 12 below.

TABLE 12 Test of specific binding and cross reactivity PNA2: PNA1:D14079 D14089 D14114 D14083 1.5 0 0 D14102 0 1 0 D14120 0 0 1.5

Example 26

Two PNA pairs, D14083-D14079 and D14096-D14089, were tested at differentPNA2 concentrations for the purpose of determining the optimalconcentration of PNA2 conjugates. The concentrations used were 0.08 μMfor PNA1 conjugates and 0.025; 0.05; 0.1 and 0.2 μM for PNA2 conjugates.

Tonsil tissues were taken through the steps 1-4, 6-8, 10, and 13-17. Theoptimal concentration of the PNA2 conjugate was 100 nM. See Table 13below.

TABLE 13 Determination of PNA2 conjugate concentration. 1% GA fixationSpecific staining PNA1 of PNA1 PNA2 0.025 μM 0.05 μM 0.1 μM 0.2 μMD14083 − D14079 1.5 2 3 2.5 D14096 − D14089 0.5 1 2 1.5

Tonsil tissues were taken through the steps 1-4, 6-8, 10, 11, and 13-17.Step 11 was omitted for tissues not fixed with 1% GA.

Fixation of PNA1 conjugates with 1% GA resulted in a stronger specificstaining than without fixation and the optimal concentration of the PNA2conjugate was now determined to be 50 nM. See Table 14 below.

TABLE 14 Effect of 1% GA fixation on the determination of PNA2 conjugateconcentration. 1% GA fixation Specific staining PNA1 of PNA1 PNA2 0.025μM 0.05 μM 0.1 μM 0.2 μM D14083 − D14079 2 2 2.5 2.5 D14083 + D14079 2.53 2.5 3

Example 27. 2-Layer Versus 3-Layer PNA Systems

This example shows the results of using a 3-layer PNA system employing aPNA¹-PNA²/Dextran conjugate adaptor unit to link the PNA1 and PNA2conjugates together. Tonsil tissues were taken through the steps 1-4,6-8, and 10-17. Step 11 was omitted for tissues not to be fixed with 1%GA. The concentration of the conjugates used was 0.08 μM for PNA1, 0.1μM (calculated based on PNA¹) for PNA¹-PNA² and 0.05 μM for PNA2.

Table 15 shows that a 3-layer system resulted in a stronger specificstaining intensity in comparison with a 2-layer system. No non-specificstaining was observed.

TABLE 15 Improvement of staining intensity by using 3 layers 1% GASpecific fixation of staining PNA1 PNA1 PNA-PNA PNA2 intensity D14096 +D14104 D14079 2 D14096 − D14104 D14079 2 D14096 − — D14089 1

The introduction of a fixation step after the application of PNA1resulted in an increase in specific staining. The specific staining wasincreased with 1+ score in the 3-layer system as shown in Table 16.Surprisingly no non-specific staining was observed despite the use of amulti-layer PNA-system.

TABLE 16 Improvement of specific staining in a 3-layer system byfixation 1% GA Specific fixation of staining PNA1 PNA1 PNA-PNA PNA2intensity D14102 + D14119 D14079 3 D14102 + D14106 D14079 3 D14102 +D14104 D14079 3 D14102 − D14119 D14079 2 D14102 − D14106 D14079 2 D14102− D14104 D14079 2

Example 28. Test of 3-Layer PNA Systems Using Different PNA¹-PNA²Concentrations in the Presence or Absence of Fixation

Tonsil tissues were taken through the steps 1-4, 6-8, and 10-17 above.Step 11 was left out for the tonsil tissues, which were not going to befixed with 1% GA. The concentration of the conjugates in the table was0.08 μM for PNA1, 0.025, 0.05, 0.1 and 0.2 μM for PNA¹-PNA² (based on[PNA¹]), and 0.05 μM for PNA2.

Fixation of PNA1 increased the specific staining intensity with 0.5+ to1+ score.

TABLE 17 The effect of using different PNA¹-PNA² concentrations.Specific staining intensity at various PNA¹-PNA² concentration PNAs 1%GA 0.025 μM 0.05 μM 0.1 μM 0.2 μM D14102 + 2.5 2.5 3 3 D14119 − 2 2 2 2D14079 D14096 + 1.5 2 2 3 D14104 − 1 1.5 2 2.5 D14079

Example 29. Effect of Using Different Concentrations of Glutardialdehyde(GA) for Fixation of PNA1

A 2-layer PNA test system was employed to study the effect of usingdifferent concentrations of GA. Tonsil tissues were taken through thesteps 1-4, 6-8, 10, 11 and 13-17. In step 11, the concentration of GAused was 0.1%, 0.3% and 1.0% respectively. The PNA pair, D14083-D14079,was used at concentrations of 0.08 μM for PNA1 and 0.05 μM for PNA2.After fixation of PNA1 conjugates, the tissues were processed with oneof three treatments listed in Table 18.

The specific staining in the 2-layer PNA system was improved when thePNA1 conjugate was fixed with at least 0.3% GA, even when the tissueswere boiled in target retrieval buffer in microwave oven for 10 min.This shows the possibility of including a strong cross linking step tothe procedure. The cross linking allows a harsh treatment with nosacrifice to the staining result.

TABLE 18 Staining intensity at different Glutardialdehyde (GA)concentration. Specific staining intensity Treatment after GA-fixationof PNA1 0.1% GA 0.3% GA 1.0% GA Wash in TBST at RT for 20 min. 1.5 1.51.5 Wash in TBST at 65° C. for 10 min. 1.0 1.5 1.5 Target retrieval(K5204) in MW oven 1.0 1.5 1.5 for 10 min.

Example 30. Comparison of a PNA-Based Detection System with an EnVision™Based Detection System

Tonsil tissues were taken through the steps 1-4, 6, 7, 9-10, and 13-17.The concentration of the conjugates was 0.08 μM for PNA1, D12102 and0.05 μM for PNA2, D12094. A negative Ig control, mouse IgG1(DakoCytomation code No. X0931) diluted 1:300 in S2022 was included inthe protocol for PNA conjugates. The EnVision™-based detection system,K5007, was used in parallel with the PNA based detection system.

The specific staining intensities obtained for the three antibodiestested and visualized with either the D12102-D12094 PNA-pair or K5007are shown in Table 19. The PNA based system showed in general a strongerspecific staining in comparison with the reference K5007.

TABLE 19 Comparison between two indirect detection systems. DilutionSpecific staining intensity Primary of primary PNA based detectionEnVision ™-based antibody antibody system detection system M3515 1:300 3— 1:900 2.5 2 1:1600 1.5 — M7240 1:400 3 — 1:1200 2.5 2 1:2400 1.5 —M0755 1:2000 3 — 1:8000 2.5 2 1:14000 1.5 — X0931 1:300 0 0

Example 31. Recognition of a Conjugated Primary Antibody by AnotherDetection System

Tonsil tissues were taken through the steps 1-4, 6, 7, 10, 11, 1S and14-17 above. 20 μL of PNA1, respectively D14122 and D14128 (0.08 and 0.3μM) were applied. Slides were cover slipped during incubation with PNA1.Then 200 μL PNA2, D14079 (0.1 μM) was applied. Samples were incubatedwith K5007 GaM:HRP complex for 30 min in parallel with PNA2 conjugatesin step 13. As a further control and for comparison, tonsil tissues weretaken through steps 1-4 and 6-8 using uncomplexed anti-BCL2, M0887,diluted 1:100 to a concentration of 0.015 μM in S2022 as primaryantibody, and visualized by incubation with K5007 GaM:HRP complex for 30min. as an alternative to the PNA2 conjugates in step 13. These slideswere then taken through steps 14-17.

Table 20 summarizes the staining results. When preparing PNA conjugateswith multiple PNAs, here illustrated by PNA1, the PNAs remainedaccessible for hybridization to complementary PNAs comprised incomponents further comprising dextran and enzymes. Conjugates comprisingmore PNA did not necessarily show improved specific staining. Instead,the amount of staining peaked and then fell as the PNA to dextran ratioincreased. For example, samples incubated with D14126 scored 1.0+, thosewith D14128 scored 2.5+, and those with D14122 scored 2.0+. Thus,D14128, with a PNA:Dextran ratio of about six, gave a stronger signalthan both D14122 with a PNA:Dex ratio of about nine as well as D14126with a PNA:Dex ratio of about three. When preparing PNA conjugates withmultiple PNAs, here illustrated by PNA1, the PNAs remained accessiblefor hybridization to complementary PNAs comprised in components furthercomprising dextran and enzymes.

This experiment also illustrates that the conjugation of multiple PNAsto an antibody may reduce the recognition of the antibody by a secondaryantibody:enzyme complex. Samples treated with anti-BCL2 antibodyconjugated with PNA1 resulted in specific staining intensities of 2.5+with PNA2 and 1.5+ with K5007 respectively. Samples treated with freeanti-BCL2 and K5007 showed a 3+ score. The signal obtained with K5007decreased with the number of PNA in the PNA1 conjugate.

TABLE 20 Significance of the amount of PNA in PNA1 conjugates onspecific staining intensity. Specific staining Specific intensity withstaining PNA/ PNA2, intensity with dextran D14079 K5007 PNA1, D14126 2.91.0 — 0.3 μM PNA1, D14128 5.6 2.5 1.5 0.3 μM PNA1, D14128 5.6 0.5 1.00.08 μM PNA1, D14122 9.5 2 1.5 0.3 μM PNA1, D14122 9.5 0.5 0 0.08 μMUnconjugated, — — 3.0 M0887

Example 32. Test of Non-Specific Binding Due to PNA2 Conjugates

Tonsil tissues were taken through the steps 1-5, 7, 13 and 14-17 above.The PNA2 conjugates tested are listed in Table 21. Replacing 2 D's inD12120 with 2 A's (D13106) reduced the non-specific staining from 3+ to1+(at 0.05 μM PNA2). When 2 G's in D13106 were replaced with 2 G_(s)'s(D13148), the non-specific staining was reduced from 1+ to 0.Reintroducing 2 D's in D13155 instead of 2 A's (D13148) increased thenon-specific staining from 1.5+ to 2.0+(at 0.2 μM PNA). Both D12120 andD13155 had 2 D's in the sequence, but the non-specific staining inD13155 did not reach the same level as in D12120, probably due to the 2G_(s)'s in D13155. The same effect of non-natural bases was seen whencomparing D12120 with D14133: the non-specific staining in D14133 didnot reach the same level as in D12120, this time probably due to 2inosines (I)'s in D14133. The replacement of 2 G's in D13122 with 2G_(s)'s (D13159) reduced the non-specific staining from 3+ to 0 (at aPNA concentration of 0.2 μM). Substitution of 1 G in D14110 with 1 Gs(D14089), reduced the non-specific staining from 1+ to 0. Equally, 1 Gin D14086 was replaced with 1 G_(s) (D14089), resulting in a reductionof the non-specific staining from 3+ to 0 (at a PNA concentration of 0.2μM).

The non-specific background staining generated by the PNA2 conjugatescould be subtly fine tuned, and ultimately completely eliminated, bybase substitution using both natural as well as non-natural bases. Thelevel of background correlated directly to the DNA/RNA affinity of thePNAs of the conjugates. This was surprising, as the conjugates have amolecular weight around 500 kDa, and the changes in the PNAs necessaryto bring about strongly reduced background in some cases were as littleas one D to A substitution (thus removing one potentially hydrogenbonding amino group) or one G to G_(s) substitution (introducing asingle carbonyl to thiocarbonyl change).

TABLE 21 Non-specific staining intensities  of due to PNA2 conjugates.Non-specific staining  intensity 0.2 μM 0.05 μM PNA2 PNA2 PNA2 SequenceD12120 3 3 TCD DGG TAC A D13106 2.5 1 TCA AGG TAC A D13148 1.5 0TCA AG_(s)G_(s) TAC A D13155 2 0 TCD DG_(s)G_(s) TAC A D14133 0.5 0TCD DII TAC A D13122 3 2 CTA AGG TCA A D13159 0 0 CTA AG_(s)G_(s) TCA AD14086 3 2.5 U_(s)CG_(s) G_(s)DD TU_(s)D GDC D14089 0 0CU_(s)G_(s) G_(s)DD TU_(s)D G_(s)DC D14110 1 0DGT CG_(s)D DG_(s)G U_(s)CU_(s) D14114 0 0DG_(s)T CG_(s)D DG_(s)G U_(s)CU_(s)

Example 33. Use of Fluorescein as a Molecular Label

Tonsil tissues were taken through the steps 1-4, 6-8, 10, and 13 (PNA2was conjugated with fluorescein) and 16 (the slides were mounted withVectashield containing DAPI). The concentration used for the conjugateswas 0.08 μM for PNA1, D13171 and 0.02, 0.05, 0.1, and 0.2 μM for PNA2,D14008 (TCD DG_(s)G_(s) TAC A). The slides were evaluated using afluorescence microscope at 40× and 100× magnifications.

The specific staining was satisfactory. This experiment demonstrated thepossibility of making PNA-fluorescein conjugates and illustrated theapplication of the present invention with a fluorescein as detectablelabel.

Example 34. Test of a PNA Pair with 10 Antibodies

A multi-block containing tissue from mammalian carcinoma, kidney, colonand two tonsils was taken through the steps 3-4, 6-8, 10, 13-17. In step8, ten different primary antibodies and a negative control mouse IgG1were used. (See table 22.) The concentration of the conjugates used was0.08 μM for PNA1, D12102 and 0.05 μM for PNA2, D12094. Visualization ofprimary reagents by the K5007 detection kit was performed in parallelaccording to the manufacturer's instructions. Two primary antibodiestargeting membranous targets were used: Monoclonal Mouse Anti-HumanCD20cy (DakoCytomation code No. M0755) and Monoclonal Mouse Anti-HumanEpithelial Membrane Antigen (DakoCytomation code No. M0613). Fiveprimary antibodies targeting cytoplasmic targets were used: MonoclonalMouse Anti-Human Cytokeratin (DakoCytomation code No. M3515), MonoclonalMouse Anti-Human Desmin (DakoCytomation code No. M0760), MonoclonalMouse Anti-Human CD68 (DakoCytomation code No. M0876), Monoclonal MouseAnti-Human BCL2 (DakoCytomation code No. 0887) and Monoclonal MouseAnti-Human CD45 LCA (DakoCytomation code No. M0701). Three primaryantibodies targeting nuclear targets were used: Monoclonal MouseAnti-Human Estrogen Receptor (DakoCytomation code No. M7047), MonoclonalMouse Anti-Human Ki-67 Antigen (DakoCytomation code No. M7240) andMonoclonal Mouse Anti-Human p27 (DakoCytomation code No. M7203). Theprimary antibodies, all products from DakoCytomation, were diluted inS2022 as indicated in Table 22.

This example shows the extended use of the PNA system employing severalprimary antibodies. Furthermore, in the majority of cases using the 10primary antibodies, visualization by the PNA based detection systemdemonstrated an improved staining as compared to the reference K5007.

TABLE 22 Comparison of the PNA based detection system with EnVision ™Primary Antibody Specific staining intensity Antibody Dilution The PNAsystem The K5007 reference M3515 1:900 2 1.5 M0876 1:800 2 2 M0887 1:5002 2 M0760 1:1200 1.5 1.5 M0701 1:1600 3 2 M0755 1:8000 1.5 1.5 M06131:6400 2.5 1.5 M7047 1:200 3 2.5 M7240 1:1200 2 1.5 M7203 1:400 2.5 1.5

Example 35. Standard Synthesis of AP-DexVS70-PNA Conjugate

Alkaline Phosphatase (“AP”) (from Calf Intestine, EIA grade) wasdialyzed overnight against 2 mM HEPES, pH 7.2; 0.1M NaCl; 0.02 mM ZnCl₂.Dextran (molecular weight 70 kDa) was activated with divinylsulfone to adegree of 92 reactive groups per dextran polymer (DexVS70).

The three components below were mixed together and placed in a waterbath at 40° C. for 30 minutes.

192.0 μL DexVS70 13.7 nmol  41.0 μL PNA   41 nmol PNA dissolved in H₂O 6.0 μL 1M NaHCO₃

108.0 μL of the DexVS70-PNA conjugate was taken out and added to amixture of:

160.0 μL AP 43.4 nmol 7.7 μL 1M NaHCO₃ 30.6 μL 20 mM Hepes, pH 7.2; 1MNaCl; 50 mM MgCl₂; 1 mM ZnCl₂

The mixture was placed in a water bath at 40° C. for 3 hours. Quenchingwas performed by adding 30.6 μL of 0.1 M ethanolamine and letting themixture stand for 30 minutes in water bath at 40° C. The product waspurified on FPLC with: Column Superdex-200, buffer: 2 mM HEPES, pH 7.2;0.1M NaCl; 5 mM MgCl₂; 0.1 mM ZnCl₂. Two fractions were collected, onewith the product and one with the residue.

In comparison to the experiment described above, another conjugate wasmade with extended conjugation time. The three components below weremixed together and placed in a water bath at 40° C. for 30 minutes.

192.0 μL DexVS70 13.7 nmol  41.0 μL PNA   41 nmol PNA dissolved in H₂O 6.0 μL 1M NaHCO₃

108.0 μL of the DexVS70-PNA conjugate was taken out and added to amixture of:

160.0 μL AP 43.4 nmol 7.7 μL 1M NaHCO₃ 30.6 μL 20 mM Hepes, pH 7.2; 1MNaCl; 50 mM MgCl₂; 1 mM ZnCl₂

The mixture was placed in a water bath at 40° C. for 5 hours. Quenchingwas performed by adding 30.6 μL 0.1 M Ethanolamine and letting themixture stand for 30 minutes in water bath at 40° C. Purification of theproduct on FPLC: Column Superdex-200, buffer: 2 mM Hepes, pH 7.2; 0.1MNaCl; 5 mM MgCl₂; 0.1 mM ZnCl₂. Two fractions were collected: One withthe product and one with the residue.

Relative absorbance PNA(Flu) (ϵ_(500nm)=73000M⁻¹) andAP(ϵ_(278nm)=140000 M⁻¹. Corrected for absorbance from PNA at 278 nm,this correction factor is due to the specific PNA and it is calculated:278/500 nm) was used to calculate the average conjugation ratio of PNA,AP and DexVS70.

AP-DexVS70-PNA, 3 hrs:

PNA/DexVS70: 1.8

AP/DexVS70: 1.8

AP-DexVS70-PNA, 5 hrs:

PNA/DexVS70: 2.0

AP/DexVS70: 2.4

Due to these results, it is recommended to follow a procedure in whichthe conjugation time (AP+DexVS70-PNA) is 5 hours.

Example 36. Synthesis and IHC Testing of an Antibody-PNA Conjugate

Part A. Testing Different Ratios of Linker to Antibody

Materials:

Antibody: CD 45 dialyzed overnight against 0.01 M Hepes 0.1 M NaClpH=7.2. SMCC: Succinimidyl-4(N-maleimidomethyl) cyclohexan-1-carboxylatemolw. 334.33. PNA: Acetyl-L₃₀-GTP-TAA-TTP-PAG-L₁₅₀-Lys(Cys)

Test 1

10 nmol CD45 was dissolved in 161 μL 0.01 M Hepes 0.1 M NaCl pH=7.2. 250nmol SMCC was dissolved in 8 μL NMP. The above components were mixed andplaced in a water bath at 30° C. for 60 minutes. The mixture waspurified on a mini-prep column (Sephadex G-25) with 0.01 M Hepes 0.1 MNaCl pH=7.2 as eluent. Fractions of 0.3 mL. By measuring absorbance at278 nm three fractions containing the product (58%) were identified.These three fractions were added to 100 nmol of a lyophilised PNA. Then1 μL 5 Di-Sodium-EDTA/water was added and the solution was mixed untildissolved and placed in a water bath at 30° C. for 30 minutes. Quenchingwas performed by adding 2 mg of Cysteine. Water bath 30° C. for 30minutes.

The product was purified on FPLC: Column SUPERDEX®-75, Buffer 0.01 MHepes 0.1 M NaCl pH 7.2. The fraction with the product was collected.Relative absorbance between PNA (ϵ_(260 nm)) and antibody (ϵ_(278 nm))was used to calculate the average conjugation ratio of PNA and antibody.PNA/CD45: 5.2. Yield 39% based on antibody.

Test 2

10 nmol CD45 was dissolved in 161 μL 0.01 M Hepes 0.1 M NaCl pH=7.2. 150nmol SMCC was dissolved in 5 μL NMP. The above components were mixed andplaced in a water bath at 30° C. for 60 minutes. The mixture waspurified on a mini-prep column (SEPHADEX® G-25) with 0.01 M Hepes 0.1 MNaCl pH=7.2 as eluent. Fractions of 0.3 mL. By measuring absorbance at278 nm three fractions containing the product (74%) were identified.

These three fractions were added to 100 nmol of a lyophilized PNA. Then1 μL 5% Di-Sodium-EDTA/water was added and the solution was mixed untildissolved and placed in a water bath at 30° C. for 30 minutes. Quenchingwas performed by adding 2 mg of cysteine. Water bath 30° C. for 30minutes.

The product was purified on FPLC: Column Superdex-75, Buffer 0.01 MHepes 0.1 M NaCl pH 7.2. The fraction with the product was collected.Relative nm) absorbance between PNA (ϵ_(260 nm)) and antibody(ϵ_(278 nm)) was used to calculate the average conjugation ratio of PNAand antibody. PNA/CD45: 3.4. Yield 55% based on antibody.

IHC Test of Conjugates

A later IHC test showed that PNA/CD45 in Test 2 gave a higher score thanthe one in Test 1. This brought us to the conclusion that the ratiobetween CD45/SMCC/PNA should be 10/150/100.

Part B. Test of Different Conjugation Times—Antibody and Linker

Materials:

Antibody: GAM (goat-anti-mouse) dialysed overnight against 0.1 M NaCl.SMCC: Succinimidyl-4(N-maleimidomethyl) cyclohexan-1-carboxylate molw.334.33. Flu-Link: Flu-L₉₀-Lys(Flu)-L₃₀-Lys(Cys)

Test 1

20 nmol GAM was dissolved in 402 μL 0.01 M Hepes 0.1 M NaCl pH=7.2. 400nmol SMCC dissolved in 13 μL NMP. The above components were mixed andplaced in a water bath at 30° C. for 1 hour. 207 μL of the mixture waspurified on a mini-prep column (SEPHADEX® G-25) with 0.01 M Hepes 0.1 MNaCl pH=7.2 as eluent. Fractions of 0.3 mL were taken. By measuringabsorbance at 278 nm, three fractions containing the product (79%) wereidentified. These three fractions were added to 200 nmol of alyophilized Flu-Link. Then 1 μL 5% di-sodium-EDTA/water was added andthe solution was mixed until dissolved and placed in a water bath at 30°C. overnight. Quenching was performed by adding 2 mg of Cysteine. Waterbath 30° C. for 30 minutes.

The product was purified on FPLC: Column SUPERDEX®-75, Buffer 0.01 MHepes 0.1 M NaCl pH 7.2. The fraction with the product was collected.Relative absorbance between Flu-Link (ϵ_(498 nm)) and antibody(ϵ_(278 nm)) was used to calculate the average conjugation ratio of PNAand antibody. Flu-Link/GAM: 7.1. Yield 55% based on antibody.

Test 2

20 nmol GAM was diluted with 402 μL 0.01 M Hepes 0.1 M NaCl pH=7.2. 400nmol SMCC was dissolved in 13 μL NMP. The above components were mixedand placed in a water bath at 30° C. for 2 hours. The rest of thesynthesis and purification was done in exactly the same procedure as for1 hour. There was a 64% yield of GAM/SMCC before adding the Flu-Link.Flu-Link/GAM: 8.7. Yield 33% based on antibody.

Part C. Test of Different Conjugation Times—Fluorophore and Linker

Materials:

Antibody: GAM dialysed overnight against 0.1 M NaCl. SMCC:Succinimidyl-4(N-maleimidomethyl) cyclohexan-1-carboxylate molw. 334.33.Flu-Link: Flu-L₉₀-Lys(Flu)-L₃₀-Lys(Cys)

Test 1

20 nmol GAM was dissolved 378 μL 0.01 M Hepes 0.1 M NaCl pH=7.2. 400nmol SMCC was dissolved in 13 μL NMP. The above components were mixedand placed in a water bath at 30° C. for 1 hour. The mixture was dividedin two and purified on two mini-prep columns (SEPHADEX® G-25) with 0.01M Hepes 0.1 M NaCl pH=7.2 as eluent. Fractions of 0.3 mL were taken. Bymeasuring absorbance at 278 nm, three fractions from each columncontaining the product (76% in all) were identified. These six fractionswere pooled, divided in two, and each added to 200 nmol of a lyophilizedFlu-Link. Then 1 μL 5% di-sodium-EDTA/water was added and the solutionwas mixed until dissolved and placed in a water bath at 30° C., one for30 minutes, the other for 60 minutes. Quenching was performed by adding2 mg of cysteine. Water bath 30° C. for 30 minutes.

The product was purified on FPLC: Column SUPERDEX®-75, Buffer 0.01 MHepes 0.1 M NaCl pH 7.2. The fractions with the product from eachpurification were collected. Relative absorbance between Flu-Link(ϵ_(498 nm)) and antibody (ϵ_(278 nm)) was used to calculate the averageconjugation ratio of PNA and antibody. 30 minutes conjugationFlu-Link/GAM: 7.0 Yield 55% based on antibody. 60 minutes conjugationFlu-Link/GAM: 6.9 Yield 52% based on antibody. The above results showthat 30 minutes conjugation between GAM/SMCC and Flu-Link is sufficient.

Example 37. Additional Tests of 2 and 3 Layer Visualization Systems

Primary mouse antibody M7240 (Dako) targeting MIB-1 was diluted to final1:150 in S2022 buffer (Dako) and applied on a multi tissue section.Following 10 minutes incubation at RT the section was washed 5 minutesusing 10× diluted S3006 buffer (Dako).

Goat-anti-mouse secondary antibody conjugated with dextran and a firstPNA sequence (GaM-dex-PNA1 (218-117)) was diluted to final concentrationof 0.08 μM (based on dextran) in BP-HEPES-buffer (1.5% BSA, 3% PEG,0.15M NaCl, 10 mM HEPES, pH 7.2) and was applied to the section.Following 10 minutes incubation at room temperature (RT), the sectionwas washed 5 minutes using 10× diluted S3006 (Dako). The sections wererinsed in deionized water. Following 10 minutes incubation in 0.5%glutaraldehyde at RT, the sections were rinsed in deionized water andwashed 5 minutes using 10× diluted S3006 (Dako).

An adaptor unit comprising dextran coupled to two different PNAsequences, one complementary to PNA1 above (PNA2) and another notcomplementary to PNA1 (PNA3), called PNA2-dex-PNA3 (218-057) was dilutedto a final concentration of 0.05 μM (dextran) in BP-HEPES-buffer (1.5%BSA, 3% PEG, 0.15M NaCl, 10 mM HEPES, pH 7.2) and was applied to thesection. Following 10 minutes incubation at RT, the section was washed 5minutes using 10× diluted S3006 (Dako). Next, a conjugate of a PNA4,complementary to PNA3 above, dextran, and the detectable label alkalinephosphatase (PNA4-dex-AP (209-177)) was diluted to final concentrationof 0.05 μM (dextran) in BAP-HEPES-buffer (1.5% BSA, 3% PEG, 0.15M NaCl,0.05% 4-aminoantipyrin, 10 mM HEPES, pH 7.2), and was applied. Following10 minutes incubation at RT, the sections were washed 5 minutes using10× diluted S3006 (Dako).

Permanent Red working solution (an aqueous Tris buffer withnaphthol-phosphate and a diazonium dye; K0640 Dako) was prepared andthen applied. Following 10 minutes incubation, the section was washed 5minutes using 10× diluted S3006 (Dako). Finally the sections werecounter stained 5 minutes using haematoxylin S3301 (Dako), rinsed indeionized water, washed 3 minutes in wash buffer, and mounted inFaramount S3025 (Dako). Result: MIB-1=1+/0.5+.

Example 38

Primary rabbit antibody A0452 (Dako) targeting CD3 was diluted to final1:100 in S2022 (Dako) and applied on a multi tissue section. Following10 minutes incubation at RT the sections were washed 5 minutes using 10×diluted S3006 (Dako).

Then, a goat-anti-rabbit secondary antibody coupled to dextran and afirst PNA sequence, PNA2a (GaR-dex-Alexander (209-127)) was diluted tofinal concentration of 0.08 μM (dextran) in BP-HEPES-buffer (1.5% BSA,3% PEG, 0.15M NaCl, 10 mM HEPES, pH 7.2) and was applied. Following 10minutes incubation at RT the sections were washed 5 minutes using 10×diluted S3006 (Dako). The sections were rinsed in deionized water.Following 10 minutes incubation in 0.5% glutaraldehyde at RT thesections were rinsed in deionized water and washed 5 minutes using 10×diluted S3006 (Dako).

Next, a complementary PNA coupled to dextran and detectable labelalkaline phosphatase (AP) (PNA2b-dex-AP (209-177) was diluted to finalconcentration of 0.05 μM (dextran) in BAP-HEPES-buffer (1.5% BSA, 3%PEG, 0.15M NaCl, 0.05% 4-aminoantipyrin, 10 mM HEPES, pH 72) and wasapplied. Following 10 minutes incubation at RT the section was washed 5minutes using 10× diluted S3006 (Dako).

Permanent Red working solution (K0640 Dako) was prepared and wasapplied. Following 10 minutes incubation the sections were washed 5minutes using 10× diluted S3006 (Dako). Finally the sections werecounter stained 5 minutes using haematoxylin S3301 (Dako), rinsed indeionized water, washed 3 minutes in wash buffer, and mounted inFaramount S3025 (Dako). Result: CD3 specific staining=1.5+ compared tonon-specific background staining of 1+. The order of detection affectsthe staining result.

Example 39. Detecting Two Targets in a Sample

General Procedural Note: Before conducting the detection experiment onformalin-fixed, paraffin-embedded (FPPE) tissue sections, the specimenshould be deparaffinized (dewaxed), rehydrated, and blocked forendogenous peroxidase activity. Some specimens should be subjected totarget retrieval using heat or enzyme digestion. Following targetretrieval, the specimens should be rinsed gently with wash buffer.

Part A. Two-Layer Detection Experiment Using Secondary Antibody Probes

In this experiment, a mouse primary antibody was used as a primarybinding agent for a specific target in a tissue sample. That antibodywas then recognized by a goat-anti-mouse-dextran-PNA conjugaterecognition unit. A different primary antibody, a rabbit antibody, wasused as a primary binding agent for a different target in the sample.That antibody was recognized by a goat-anti-rabbit-dextran-PNArecognition unit. One reaction was visualized by a PNA-dextran-HRP(horse-radish peroxidase) detection unit and the other reaction wasvisualized by a PNA-dextran-AP (alkaline phosphatase) detection unit.PNA sequences 1 and 2 and sequences 3 and 4, respectively, specificallyhybridize to each other.

Primary mouse antibody M3515 (Dako) targeting Cytokeratin and primaryrabbit antibody Z0311 (Dako) targeting S100 were diluted 1:50 and 1:100in S2022 buffer (Dako), respectively. The antibodies were appliedsimultaneously on multi tissue sections. Following 10 minutes incubationat RT the sections were washed 5 minutes using 10× diluted S3006 buffer(Dako). Goat-anti-mouse-dextran-PNA1 (GaM-dex-PNA1) andgoat-anti-rabbit-dextran-PNA3 (GaR-dex-PNA3) were both diluted to afinal concentration of 0.08 μM (dextran) in BP-HEPES-buffer (1.5% BSA,3% PEG, 0.15M NaCl, 10 mM HEPES, pH 7.2). The two conjugates wereapplied simultaneously on the sections. Following 10 minutes incubationat room temperature (RT), the sections were washed 5 minutes using 10×diluted S3006 (Dako). The sections were rinsed in deionized water.

The samples were then incubated for 10 minutes in 0.5% glutaraldehyde atRT and then rinsed in deionized water and washed 5 minutes using 10×diluted S3006 (Dako). PNA2-dex-HRP and PNA4-dex-AP were both diluted tofinal concentration of 0.05 μM (dextran) in BAP-HEPES-buffer (1.5% BSA,3% PEG, 0.15M NaCl, 0.05% 4-aminoantipyrin, 10 mM HEPES, pH 7.2). Thetwo conjugates were applied simultaneously on the sections. Following 10minutes incubation at RT the sections were washed 5 minutes using 10×diluted S3006 (Dako). Permanent Red working solution (K0640 Dako) andDAB+ working solution (an aqueous imidazole buffer with hydrogenperoxide and DAB; K3468 Dako) were prepared.

The reactions were detected with one of the following methods.

Detection Method 1:

Permanent Red working solution was applied. Following 10 minutesincubation the sections were washed 5 minutes using 10× diluted S3006(Dako). Then DAB+ working solution was applied and following 10 minutesincubation the sections were washed 5 minutes using deionized water.Finally the sections were counter stained 5 minutes using haematoxylinS3301 (Dako), rinsed in deionized water, washed 3 minutes in washbuffer, and mounted in Faramount S3025 (Dako).

Detection Method 2:

DAB+ working solution was applied. Following 10 minutes incubation thesections were washed 5 minutes using 10× diluted S3006 (Dako). ThenPermanent Red working solution was applied and following 10 minutesincubation the sections were washed 5 minutes using deionized water.Finally the sections were counter stained 5 minutes using haematoxylinS3301 (Dako), rinsed in deionized water, washed 3 minutes in washbuffer, and mounted in Faramount S3025 (Dako).

Result: Cytokeratin=HRP=3+ specific staining and 0 background staining,S100=AP=3+ specific staining and 0 background staining. The order ofdetection affects the staining result. If detection method 1 is usedthen Permanent Red dominates. If detection method 2 is used then DAB+dominates.

Part B. Two-Layer Detection Experiment Using Antibodies as Probes

Primary mouse antibody M3515 (Dako) targeting Cytokeratin and primaryrabbit antibody Z0311 (Dako) targeting S100 were diluted to final 1:50and 1:400 in S2022 (Dako), respectively. The antibody mixture wasapplied on multi-tissue sections. Following 10 minutes incubation at RTthe sections were washed 5 minutes using 10× diluted S3006 (Dako).GaM-dex-PNA1 (209-149) and GaR-dex-PNA2 (209-127) were both diluted tofinal concentration of 0.08 μM (dextran) in BP-HEPES-buffer (1.5% BSA,3% PEG, 0.15M NaCl, 10 mM HEPES, pH 7.2). The two conjugates wereapplied simultaneously on the sections.

Following 10 minutes incubation at RT the sections were washed 5 minutesusing 10× diluted S3006 (Dako). The sections were rinsed in deionizedwater. Following 10 minutes incubation in 1% glutaraldehyde at RT thesections were rinsed in deionized water and washed 5 minutes using 10×diluted S3006 (Dako). PNA2-dex-HRP (209-157) and PNA4-dex-AP (209-177)were both diluted to final concentration of 0.05 μM/dex inBAP-HEPES-buffer (1.5% BSA, 3% PEG, 0.15M NaCl, 0.05% 4-aminoantipyrin,10 mM HEPES, pH 7.2). The two conjugates were applied simultaneously onthe sections. Following 10 minutes incubation at RT the sections werewashed 5 minutes using 10× diluted S3006 (Dako). Permanent Red workingsolution (K0640 Dako) and DAB+ working solution (K3468 Dako) wereprepared.

The reactions were detected with one of the following methods.

Detection Method 1:

Permanent Red working solution was applied. Following 10 minutesincubation the sections were washed 5 minutes using 10× diluted S3006(Dako). Then DAB+ working solution was applied and following 10 minutesincubation the sections were washed 5 minutes using deionized water.Finally the sections were counter stained 5 minutes using haematoxylinS3301 (Dako), rinsed in deionized water, washed 3 minutes in washbuffer, and mounted in Faramount S3025 (Dako).

Detection Method 2:

DAB+ working solution was applied. Following 10 minutes incubation thesections were washed 5 minutes using 10× diluted S3006 (Dako). ThenPermanent Red working solution was applied and following 10 minutesincubation the sections were washed 5 minutes using deionized water.Finally the sections were counter stained 5 minutes using haematoxylinS3301 (Dako), rinsed in deionized water, washed 3 minutes in washbuffer, and mounted in Faramount S3025 (Dako).

Result: Using detection method 1: Cytokeratin=HRP=2.5+ specific stainingand 0 background staining, S100=AP=2.5+ specific staining and 0background staining. Using detection method 2: Cytokeratin=HRP=3+specific staining and 0.5+ background staining, S100=AP=3+ specificstaining and 0 background staining. The order of detection affects thestaining result.

Example 40. Further 2 and 3 Layer Systems for Detection of MultipleTargets

Part A. Combined Two and Three-Layer System

In this example, a mouse antibody primary binding agent was recognizedby a GaM-dex-PNA1 and a rabbit antibody primary binding agent wasrecognized by GaR-dex-PNA2. One reaction was detected by aPNA-dex-Enzyme1 conjugate and the other by a PNA-dex-PNA adaptor unitand then a PNA-dex-Enzyme2 conjugate. PNA1 recognizes PNA2 while PNA3recognizes PNA4. The enzymes used were HRP and AP, bringing alongrespectively a brown and red end-product within the same tissue section.The PNA-dex-PNA adaptor unit adds a third layer to the detection system.

Primary mouse antibody M7240 (Dako) targeting MIB-1 and primary rabbitantibody A0452 (Dako) targeting CD3 were diluted to final 1:150 and1:100 in S2022 (Dako), respectively. The antibody mixture was applied onmulti tissue sections. Following 10 minutes incubation at RT thesections were washed 5 minutes using 10× diluted S3006 (Dako).

GaM-dex-PNA1 (218-117) and GaR-dex-PNA3 (209-127) were both diluted tofinal concentration of 0.08 μM (dextran) in BP-HEPES-buffer (1.5% BSA,3% PEG, 0.15M NaCl, 10 mM HEPES, pH 7.2). The two conjugates wereapplied simultaneously on the sections. Following 10 minutes incubationat RT the sections were washed 5 minutes using 10× diluted S3006 (Dako).The sections were rinsed in deionized water. Following 10 minutesincubation in 0.5% glutaraldehyde at RT the sections were rinsed indeionized water and washed 5 minutes using 10× diluted S3006 (Dako).

PNA4-dex-HRP (218-021) was diluted to final concentration of 0.05 μM(dextran) in BAP-HEPES-buffer (1.5% BSA, 3% PEG, 0.15M NaCl, 0.05%4-aminoantipyrin, 10 mM HEPES, pH 7.2) and applied on the sections.Following 10 minutes incubation at RT the sections were washed 5 minutesusing 10× diluted S3006 (Dako). PNA2-dex-PNA3 (218-057) amplificationunit was diluted to final concentration of 0.05 μM (dextran) inBP-HEPES-buffer (1.5% BSA, 3% PEG, 0.15M NaCl, 10 mM HEPES, pH 7.2) andapplied on the sections. Following 10 minutes incubation at RT thesections were washed 5 minutes using 10× diluted S3006 (Dako).PNA4-dex-AP (209-177) was diluted to final concentration of 0.05 μM/dexin BAP-HEPES-buffer (1.5% BSA, 3% PEG, 0.15M NaCl, 0.05%4-aminoantipyrin, 10 mM HEPES, pH 7.2) and applied on the sections.Following 10 minutes incubation at RT the sections were washed 5 minutesusing 10× diluted S3006 (Dako). Permanent Red working solution (K0640Dako) and DAB+ working solution (K3468 Dako) were prepared.

The reactions were detected with one of the following methods.

Detection Method 1:

Permanent Red working solution was applied. Following 10 minutesincubation the sections were washed 5 minutes using 10× diluted S3006(Dako). Then DAB+ working solution was applied and following 10 minutesincubation the sections were washed 5 minutes using deionized water.Finally the sections were counter stained 5 minutes using haematoxylinS3301 (Dako), rinsed in deionized water, washed 3 minutes in washbuffer, and mounted in Faramount S3025 (Dako).

Detection Method 2:

DAB+ working solution was applied. Following 10 minutes incubation thesections were washed 5 minutes using 10× diluted S3006 (Dako). ThenPermanent Red working solution was applied and following 10 minutesincubation the sections were washed 5 minutes using deionized water.Finally the sections were counter stained 5 minutes using haematoxylinS3301 (Dako), rinsed in deionized water, washed 3 minutes in washbuffer, and mounted in Faramount S3025 (Dako).

Result: CD3=2-layer experiment=HRP=3+ specific and 0 backgroundstaining, MIB-1=3-layer experiment=AP=2+ specific and 1.5+ backgroundstaining. The order of detection affects the staining result.

Part B.

Primary mouse antibody M7240 (Dako) targeting MIB-1 and primary rabbitantibody A0452 (Dako) targeting CD3 were diluted to final 1:150 and1:100 in S2022 (Dako), respectively. The antibody mixture was applied onmulti tissue sections. Following 10 minutes incubation at RT thesections were washed 5 minutes using 10× diluted S3006 (Dako).

GaM-dex-PNA1 (218-117) and GaR-dex-PNA3 (209-127) were both diluted tofinal concentration of 0.08 μM (dextran) in BP-HEPES-buffer (1.5% BSA,3% PEG, 0.15M NaCl, 10 mM HEPES, pH 7.2). The two conjugates wereapplied simultaneously on the sections. Following 10 minutes incubationat RT the sections were washed 5 minutes using 10× diluted S3006 (Dako).The sections were rinsed in deionized water. Following 10 minutesincubation in 0.5% glutaraldehyde at RT the sections were rinsed indeionized water and washed 5 minutes using 10× diluted S3006 (Dako).

PNA4-dex-AP (209-177) was diluted to final concentration of 0.05 μM(dextran) in BAP-HEPES-buffer (1.5% BSA, 3% PEG, 0.15M NaCl, 0.05%4-aminoantipyrin, 10 mM HEPES, pH 7.2) and applied on the sections.Following 10 minutes incubation at RT the sections were washed 5 minutesusing 10× diluted S3006 (Dako). PNA2-dex-PNA3 (218-057) was diluted tofinal concentration of 0.05 μM (dextran) in BP-HEPES-buffer (1.5% BSA,3% PEG, 0.15M NaCl, 10 mM HEPES, pH 7.2) and applied on the sections.Following 10 minutes incubation at RT the sections were washed 5 minutesusing 10× diluted S3006 (Dako).

PNA4-dex-HRP (218-021) was diluted to final concentration of 0.05(dextran) in BAP-HEPES-buffer (1.5% BSA, 3% PEG, 0.15M NaCl, 0.05%4-aminoantipyrin, 10 mM HEPES, pH 7.2) and applied on the sections.Following 10 minutes incubation at RT the sections were washed 5 minutesusing 10× diluted S3006 (Dako).

Permanent Red working solution (K0640 Dako) and DAB+ working solution(K3468 Dako) were prepared. The reactions were detected with one of thefollowing methods.

Detection Method 1:

Permanent Red working solution was applied. Following 10 minutesincubation the sections were washed 5 minutes using 10× diluted S3006(Dako). Then DAB+ working solution was applied and following 10 minutesincubation the sections were washed 5 minutes using deionized water.

Finally the sections were counter stained 5 minutes using haematoxylinS3301 (Dako), rinsed in deionized water, washed 3 minutes in washbuffer, and mounted in Faramount S3025 (Dako).

Detection Method 2:

DAB+ working solution was applied. Following 10 minutes incubation thesections were washed 5 minutes using 10× diluted S3006 (Dako). ThenPermanent Red working solution was applied and following 10 minutesincubation the sections were washed 5 minutes using deionized water.Finally the sections were counter stained 5 minutes using haematoxylinS3301 (Dako), rinsed in deionized water, washed 3 minutes in washbuffer, and mounted in Faramount S3025 (Dako).

Result: Using detection method 1: CD3=2-layer experiment=AP=2+ specificand 0 non-specific, background staining, MIB-1=3-layerexperiment=HRP=1.5+ specific and 0 background staining. Using detectionmethod 2: CD3=2-layer experiment=AP=3+ specific and 1.5+ nonspecificstaining, MIB-1=3-layer experiment=HRP=1.5+ specific and 1+ backgroundstaining. The order of detection affects the staining result.

Example 41. Further Multi-Target Detection Experiment

This example presents a 2-layer detection of two targets in whichmouse-Ab-dex-PNA is recognized by PNA-dex-Enzyme1 and rabbit-Ab-dex-PNAis recognized by PNA-dex-Enzyme2. The enzymes are HRP and AP bringingalong respectively a brown and red end-product within the same tissuesection. As in preceding examples, PNA1 and 2 specifically hybridize, asdo PNA3 and 4.

CD3-dex-PNA1 (D16043) and MIB-1-dex-PNA2 (218-097) were both diluted tofinal concentration of 0.1 μM (dextran) in BP-HEPES-buffer (1.5% BSA, 3%PEG, 0.15M NaCl, 10 mM HEPES, pH 7.2). The two conjugates were appliedsimultaneously on the sections. Following 10 minutes incubation at RTthe sections were washed 5 minutes using 10× diluted S3006 (Dako).

PNA2-dex-HRP (209-141) and PNA4-dex-AP (209-177) were diluted to finalconcentration of 0.2 μM (dextran) and 0.05 μM (dextran) inBAP-HEPES-buffer (1.5% BSA, 3% PEG, 0.15M NaCl, 0.05% 4-aminoantipyrin,10 mM HEPES, pH 7.2), respectively. The two conjugates were appliedsimultaneously on the sections. Following 10 minutes incubation at RTthe sections were washed 5 minutes using 10× diluted S3006 (Dako).Permanent Red working solution (K0640 Dako) and DAB+ working solution(K3468 Dako) were prepared.

The reactions were detected with one of the following methods.

Detection Method 1:

Permanent Red working solution was applied. Following 10 minutesincubation the sections were washed 5 minutes using 10× diluted S3006(Dako). Then DAB+ working solution was applied and following 10 minutesincubation the sections were washed 5 minutes using deionized water.Finally the sections were counter stained 5 minutes using haematoxylinS3301 (Dako), rinsed in deionized water, washed 3 minutes in washbuffer, and mounted in Faramount S3025 (Dako).

Detection Method 2:

DAB+ working solution was applied. Following 10 minutes incubation thesections were washed 5 minutes using 10× diluted S3006 (Dako). ThenPermanent Red working solution was applied and following 10 minutesincubation the sections were washed 5 minutes using deionized water.Finally the sections were counter stained 5 minutes using haematoxylinS3301 (Dako), rinsed in deionized water, washed 3 minutes in washbuffer, and mounted in Faramount S3025 (Dako).

Result: Using detection method 1: CD3=HRP=2+ specific and 0non-specific, background staining, MIB-1=AP=3+ specific and 0 backgroundstaining. Using detection method 2: CD3=HRP=2+ specific and 0.5+background staining, MIB-1=AP=2.5+ specific and 0 background staining.The order of detection affects the staining result.

Example 42. 3-Layer Detection System for Detecting MIB-1 Primary MouseAntibody

Aim:

To show that the MIB-1 primary mouse antibody can be detected in a3-layer system.

Experimental Steps:

Primary mouse antibody M7240 (Dako) targeting MIB-1 was diluted to afinal 1:150 in S2022 buffer (Dako) and applied on a multi tissuesection. Following 10 minutes incubation at RT the section was washed 5minutes using 10× diluted S3006 (Dako). GaM-dex-PNA1 was diluted to afinal concentration of 0.08 μM (dextran) in BP-HEPES-buffer (1.5% BSA,3% PEG, 0.15M NaCl, 10 mM HEPES, pH 7.2) and was applied. Following 10minutes incubation at RT the section was washed 5 minutes using 10×diluted S3006 buffer (Dako). The sections were rinsed in deionizedwater.

Following 10 minutes incubation in 0.5% glutaraldehyde at RT thesections were rinsed in deionized water and washed 5 minutes using 10×diluted S3006 (Dako). PNA2-dex-PNA3 was diluted to a final concentrationof 0.05 μM (dextran) in BP-HEPES-buffer (1.5% BSA, 3% PEG, 0.15M NaCl,10 mM HEPES, pH 7.2) and was applied. (PNA2 hybridizes to PNA1 whilePNA3 hybridizes to PNA4.) Following 10 minutes incubation at RT thesection was washed 5 minutes using 10× diluted S3006 (Dako).

PNA4-dex-HRP was diluted to final concentration of 0.05 μM (dextran) inBAP-HEPES-buffer (1.5% BSA, 3% PEG, 0.15M NaCl, 0.05% 4-aminoantipyrin,10 mM HEPES, pH 7.2) and was applied. Following 10 minutes incubation atRT the sections were washed 5 minutes using 10× diluted S3006 (Dako).

Prepared DAB+ working solution (Dako K3468) was applied. Following 10minutes incubation the sections were washed 5 minutes deionized water.Finally the sections were counter stained 5 minutes using haematoxylinS3301 (Dako), rinsed in deionized water, washed 3 minutes in washbuffer, and mounted in Faramount S3025 (Dako).

Result:

The brown end product of the HRP reaction visualize the specific nuclearMIB-1 staining of proliferating cells. Staining intensity score 2.5+ andbackground score 1+.

Example 43. 2-Layer IHC Detection Test Comparing Orientation of PNAHybridization

Aim:

To use 2-layer HRP detection to test and compareGaM-dex-PNA1+PNA2-dex-HRP and GaM-dex-PNA2+PNA1-dex-HRP.

Unit No. Unit No. GaM-dex-PNA PNA-dex-HRP Specific score Backgroundscore 218-117 209-141 1.5+ 0 218-163 218-121 0.5+ 0

Experimental Steps:

Primary mouse antibody M3515 (Dako) targeting CK was diluted to final1:200 in S2022 (Dako) and applied on a multi tissue section. Following10 minutes incubation at RT the section was washed 5 minutes using 10×diluted S3006 (Dako). GaM-dex-PNA (218-117 or 218-163) was diluted tofinal concentration of 0.08 μM/dex in BP-HEPES-buffer (1.5% BSA, 3% PEG,0.15M NaCl, 10 mM HEPES, pH 7.2) and was applied. Following 10 minutesincubation at RT the section was washed 5 minutes using 10× dilutedS3006 (Dako). The sections were rinsed in deionized water. Following 10minutes incubation in 0.5% glutaraldehyde at RT the sections were rinsedin deionized water and washed 5 minutes using 10× diluted S3006 (Dako).

PNA-dex-HRP (209-141 or 218-121) was diluted to final concentration of0.05 μM/dex in BAP-HEPES-buffer (1.5% BSA, 3% PEG, 0.15M NaCl, 0.05%4-aminoantipyrin, 10 mM HEPES, pH 7.2) and was applied. Following 10minutes incubation at RT the sections were washed 5 minutes using 10×diluted S3006 (Dako).

Prepared DAB+ working solution (Dako K3468) was applied. Following 10minutes incubation the sections were washed 5 minutes deionized water.Finally the sections were counter stained 5 minutes using haematoxylinS3301 (Dako), rinsed in deionized water, washed 3 minutes in washbuffer, and mounted in Faramount S3025 (Dako).

Result:

The brown end product of the HRP reaction visualize the specificcytokeratin staining of epithelia cells and show that performance dependon which one of the PNA sequences from a PNA pair were used whencomposing the recognition and detection unit.

Example 44. 2-Layer IHC Testing of Recognition Units with DifferentLinker Length

Aim:

to use 2-layer HRP detection to test and compare recognition units withdifferent linker length (L150, L300, L540).

Unit No. Linker length Specific score Background score 209-033 L150 2.5+1+ 209-029 L300 2.5+ 1+ 195-147 L540 2+   0  

Experimental Steps:

Primary mouse antibody M3515 (Dako) targeting CK was diluted to final1:200 in S2022 (Dako) and applied on a multi tissue section. Following10 minutes incubation at RT the section was washed 5 minutes using 10×diluted S3006 (Dako).

GaM-dex-PNA1 (209-033, 209-029, or 195-147) was diluted to a finalconcentration of 0.08 μM/dex in BP-HEPES-buffer (1.5% BSA, 3% PEG, 0.15MNaCl, 10 mM HEPES, pH 7.2) and was applied. Following 10 minutesincubation at RT the section was washed 5 minutes using 10× dilutedS3006 (Dako). The sections were rinsed in deionized water. Following 10minutes incubation in 0.5% glutaraldehyde at RT the sections were rinsedin deionized water and washed 5 minutes using 10× diluted S3006 (Dako).

PNA2-dex-HRP (209-041) was diluted to final concentration of 0.05 μM/dexin BAP-HEPES-buffer (1.5% BSA, 3% PEG, 0.15M NaCl, 0.05%4-aminoantipyrin, 10 mM HEPES, pH 7.2) and was applied. Following 10minutes incubation at RT the sections were washed 5 minutes using 10×diluted S3006 (Dako).

Prepared DAB+ working solution (Dako K3468) was applied. Following 10minutes incubation the sections were washed 5 minutes deionized water.Finally the sections were counter stained 5 minutes using haematoxylinS3301 (Dako), rinsed in deionized water, washed 3 minutes in washbuffer, and mounted in Faramount S3025 (Dako).

Result:

The brown end product of the HRP reaction visualize the specificcytokeratin staining of epithelia cells and show no significantdifference in performance when comparing recognition units havingdifferent linker length.

Example 45. 2-Layer IHC Testing of Recognition Units with DifferentDextran Size

Aim:

to use 2-layer HRP detection to test and compare recognition units withdifferent dextran size (dex70 and dex150).

Unit No. Dextran size Specific score Background score 195-147 Dex70  2+0   195-151 Dex150 2+ 1+

Experimental Steps:

Primary mouse antibody M3515 (Dako) targeting CK was diluted to final1:200 in S2022 (Dako) and applied on a multi tissue section. Following10 minutes incubation at RT the section was washed 5 minutes using 10×diluted S3006 (Dako).

GaM-dex-PNA1 (195-147 or 195-151) was diluted to final concentration of0.08 μM/dex in BP-HEPES-buffer (1.5% BSA, 3% PEG, 0.15M NaCl, 10 mMHEPES, pH 7.2) and was applied. Following 10 minutes incubation at RTthe section was washed 5 minutes using 10× diluted S3006 (Dako). Thesections were rinsed in deionized water. Following 10 minutes incubationin 0.5% glutaraldehyde at RT the sections were rinsed in deionized waterand washed 5 minutes using 10× diluted S3006 (Dako).

PNA2-dex-HRP (209-041) diluted to final concentration of 0.05 μM/dex inBAP-HEPES-buffer (1.5% BSA, 3% PEG, 0.15M NaCl, 0.05% 4-aminoantipyrin,10 mM HEPES, pH 7.2) was applied. Following 10 minutes incubation at RTthe sections were washed 5 minutes using 10× diluted S3006 (Dako).

Prepared DAB+ working solution (Dako K3468) was applied. Following 10minutes incubation the sections were washed 5 minutes deionized water.Finally the sections were counter stained 5 minutes using haematoxylinS3301 (Dako), rinsed in deionized water, washed 3 minutes in washbuffer, and mounted in Faramount S3025 (Dako).

Result:

The brown end product of the HRP reaction visualize the specificcytokeratin staining of epithelia cells and show no significantdifference in performance when comparing recognition units havingdifferent dextran size.

Example 46. 2-Layer IHC Testing of Detection Units with Different Numberof Linker-PNA Attached

Aim:

to use 2-layer HRP detection to test and compare detection units withdifferent number of PNA per dextran (0.8 PNA/dex and 1.5 PNA/dex).

Unit No. PNA/dex Specific score Background score 195-051 0.8 3+ 0.5+D15008 1.5 3+ 0.5+

Experimental Steps:

Primary mouse antibody M3515 (Dako) targeting CK was diluted to final1:200 in S2022 (Dako) and applied on a multi tissue section. Following10 minutes incubation at RT the section was washed 5 minutes using 10×diluted S3006 (Dako).

GaM-dex-PNA1 (195-047) diluted to final concentration of 0.08 μM/dex inBP-HEPES-buffer (1.5% BSA, 3% PEG, 0.15M NaCl, 10 mM HEPES, pH 7.2) wasapplied. Following 10 minutes incubation at RT the section was washed 5minutes using 10× diluted S3006 (Dako). The sections were rinsed indeionized water. Following 10 minutes incubation in 0.5% glutaraldehydeat RT the sections were rinsed in deionized water and washed 5 minutesusing 10× diluted S3006 (Dako).

PNA2-dex-HRP (195-051 or D15008) diluted to final concentration of 0.05μM/dex in BAP-HEPES-buffer (1.5% BSA, 3% PEG, 0.15M NaCl, 0.05%4-aminoantipyrin, 10 mM HEPES, pH 7.2) was applied. Following 10 minutesincubation at RT the sections were washed 5 minutes using 10× dilutedS3006 (Dako).

Prepared DAB+ working solution (Dako K3468) was applied. Following 10minutes incubation the sections were washed 5 minutes deionized water.Finally the sections were counter stained 5 minutes using haematoxylinS3301 (Dako), rinsed in deionized water, washed 3 minutes in washbuffer, and mounted in Faramount S3025 (Dako).

Result:

The brown end product of the HRP reaction visualize the specificcytokeratin staining of epithelia cells and show no significantdifference in performance when comparing detection units havingdifferent number of PNA/dex.

Example 47. 2-Layer IHC Testing Comparing Recognition and DetectionUnits Having “Linker-PNA” or “Linker-PNA-Linker Tail” Attached

Aim:

to use 2-layer HRP detection to test and compare recognition anddetection units having PNA sequences without and with “linker tail”.

Unit No. GaM-dex- Unit No. PNA- Specific PNA tail dex-HRP tail scoreBackground score 218-113 No 218-021 No 3+ 1+   D16074 Yes 218-021 No 3+0.5+ 218-113 No D16076 Yes 3+ 0.5+ D16074 Yes D16076 Yes 4+ 1.5+

Experimental Steps:

Primary mouse antibody M3515 (Dako) targeting CK was diluted to final1:200 in S2022 (Dako) and applied on a multi tissue section. Following10 minutes incubation at RT the section was washed 5 minutes using 10×diluted S3006 (Dako). GaM-dex-PNA (218-113 or D16074) diluted to finalconcentration of 0.08 μM/dex in BP-HEPES-buffer (1.5% BSA, 3% PEG, 0.15MNaCl, 10 mM HEPES, pH 7.2) was applied. Following 10 minutes incubationat RT the section was washed 5 minutes using 10× diluted S3006 (Dako).The sections were rinsed in deionized water. Following 10 minutesincubation in 0.5% glutaraldehyde at RT the sections were rinsed indeionized water and washed 5 minutes using 10× diluted S3006 (Dako).

PNA-dex-HRP (218-021 or D16076) diluted to final concentration of 0.05μM/dex in BAP-HEPES-buffer (1.5% BSA, 3% PEG, 0.15M NaCl, 0.05%4-aminoantipyrin, 10 mM HEPES, pH 7.2) was applied. Following 10 minutesincubation at RT the sections were washed 5 minutes using 10× dilutedS3006 (Dako).

Prepared DAB+ working solution (Dako K3468) was applied. Following 10minutes incubation the sections were washed 5 minutes deionized water.Finally the sections were counter stained 5 minutes using haematoxylinS3301 (Dako), rinsed in deionized water, washed 3 minutes in washbuffer, and mounted in Faramount S3025 (Dako).

Result:

The brown end product of the HRP reaction visualize the specificcytokeratin staining of epithelia cells and show that performance dependon the presence of a “linker tail” on the PNA sequence. A “linker-tail”on the PNA sequence may influence both specific score and backgroundscore.

Example 48. 2-Layer IHC Testing Comparing Recognition and DetectionUnits Having “Linker-PNA” or “Linker-PNA-Charge” Attached

Aim:

to use 2-layer HRP detection to test and compare recognition anddetection units having PNA sequences without and with charge.

Unit No. Unit No. GaM-dex- PNA-dex- Specific Background PNA charge HRPcharge score score D15078 No D15069 No 0.5+ 0   209-149 Yes 209-157 Yes3+   1+

Experimental Steps:

Primary mouse antibody M3515 (Dako) targeting CK was diluted to final1:200 in S2022 (Dako) and applied on a multi tissue section. Following10 minutes incubation at RT the section was washed 5 minutes using 10×diluted S3006 (Dako).

GaM-dex-PNA (D15078 or 209-149) diluted to final concentration of 0.08μM/dex in BP-HEPES-buffer (1.5% BSA, 3% PEG, 0.15M NaCl, 10 mM HEPES, pH7.2) was applied. Following 10 minutes incubation at RT the section waswashed 5 minutes using 10× diluted S3006 (Dako). The sections wererinsed in deionized water. Following 10 minutes incubation in 0.5%glutaraldehyde at RT the sections were rinsed in deionized water andwashed 5 minutes using 10× diluted S3006 (Dako).

PNA-dex-HRP (D15069 or 209-157) diluted to final concentration of 0.05μM/dex in BAP-HEPES-buffer (1.5% BSA, 3% PEG, 0.15M NaCl, 0.05%4-aminoantipyrin, 10 mM HEPES, pH 7.2) was applied. Following 10 minutesincubation at RT the sections were washed 5 minutes using 10× dilutedS3006 (Dako).

Prepared DAB+ working solution (Dako K3468) was applied. Following 10minutes incubation the sections were washed 5 minutes deionized water.Finally the sections were counter stained 5 minutes using haematoxylinS3301 (Dako), rinsed in deionized water, washed 3 minutes in washbuffer, and mounted in Faramount S3025 (Dako).

Result:

The brown end product of the HRP reaction visualize the specificcytokeratin staining of epithelia cells and show that performance dependon the presence of charge on the PNA sequence. Charge on the PNAsequences within a PNA pair may influence both specific score andbackground score.

Example 49. Method of Synthesizing Mono and 2,4-Diamino-Pyrimidine-5-ylPNA Monomers

2,4-diamino-pyrimidine-5-yl may be introduced into DNA-oligomers bymethods known in the art (e.g. S. A. Benner et al., Nucleic AcidResearch 24(7): 1308-1313 (1996)). A corresponding PNA oligomer isprepared by chlorinating pyrimidine-5-acetic acid to yield2-chloro-pyrimidine-5-acetic acid, 4-chloro-pyrimidine-5-acetic acid,and 2,4-dichloro-pyrimidine-5-acetic acid. Separation of isomers,followed by high temperature and pressure treatment with ammonia, givesthe three corresponding amino-pyrimidine derivatives (see FIG. 20). Theamino-pyrimidine derivatives are separated and amino-protected, thencoupled to a protected PNA backbone ester. Ester hydrolysis results inPNA monomers for production of PNA oligomers containing 2-amino;4-amino; and/or 2,4-diamino pyrimidine-5-yl bases.

Example 50. Synthesis of Xanthine and Thio-Xanthine-Coupled PNA Monomers

Xanthine, 2-thio-xanthine, and 6-thio-xanthine are commerciallyavailable, for instance, from ScienceLab.com. Further, S. A. Benner etal., Nucleic Acid Research 24(7): 1308-1313 (1996) teaches thepreparation of a xanthosine-DNA monomer, including a less acidic andpreferable 7-deaza analog, and notes the preferred protection of bothoxygens during solid phase synthesis.

Xanthine PNA-monomers, as well as 2-thio and 6-thio xanthine monomers,are prepared by:

-   -   1. Protecting both oxygens or both oxygen and sulphur with        appropriate protection groups such as (possibly substituted)        benzyl.    -   2. Alkylating at N-9 with ethyl bromoacetate. (Separating N-7        alkylated byproduct.)    -   3. Hydrolyzing the ethyl ester.    -   4. HBTU or Carbodiimide-mediated coupling of the        nucleobase-acids to 2-Boc-aminoethyl-ethylglycinate.    -   5. Hydrolyzing the resulting monomer ester to the monomer free        acid.    -   6. The resulting monomers may be used in Merrifield solid phase        synthesis of xanthine, 2-thio-xanthine and        6-thio-xanthine-containing PNAs.

Yet other embodiments of the invention will be apparent to those skilledin the art from consideration of the specification and practice of theinvention disclosed herein. It is intended that the specification andexamples be considered as exemplary only.

What is claimed is:
 1. A composition comprising at least one recognitionunit and at east one detection unit wherein: a) each unit independentlycomprises at least one nucleic acid analog segment; b) at least onenucleic acid analog segment of the recognition unit specificallyhybridizes to at least one nucleic acid analog segment of the detectionunit; c) the recognition unit further comprises at least one probe whichrecognizes at least one target in a sample; d) the detection unitfurther comprises at least one detectable label, and the recognitionunit does not comprise a detectable label; e) the at least one nucleicacid analog segment on the recognition unit that specifically hybridizesto the at least one nucleic acid analog segment on the detection unitdoes not specifically hybridize to the probe, does not specificallyhybridize to the detectable label, and does not specifically hybridizeto the target; and f) the detection unit does not specifically hybridizeto the probe, does not specifically hybridize to the detectable label,and does not specifically hybridize to the target; wherein the sample isan in situ hybridization (ISH) sample.
 2. The composition according toclaim 1, wherein at least one nucleic acid analog segment comprises atleast one non-natural base.
 3. The composition according to claim 2,wherein the non-natural base is chosen, from xanthine, a thio-xanthine,inosine, diaminopurine, pyrimidinone, a thiouracil, 2-thio-guanine, and2-amino-6-thioxopurine.
 4. The composition according to claim 2, whereinat least one nucleic acid analog segment comprises a peptide-nucleicacid (PNA) backbone.
 5. The composition of claim 1, wherein the probe isa nucleic acid or nucleic acid analog segment.
 6. The compositionaccording to claim 1, wherein each unit comprises at least two nucleicacid analog segments that specifically hybridize to at least one otherunit but do not specifically hybridize to the probe, detectable label,or target; and wherein said at least two nucleic acid analog segmentsoptionally comprise different nucleobase sequences.
 7. The compositionaccording to claim 1, wherein at least one nucleic acid analog segmenton one of the units is capable of specifically hybridizing to at leasttwo nucleic acid analog segments on another unit, each comprising adifferent nucleobase sequence.
 8. The composition according to claim 1,wherein the probe recognizes the target indirectly by binding to aprimary, secondary, or tertiary binding agent.
 9. The compositionaccording to claim 1, wherein at least one unit further comprises atleast one polymer attaching the at least one nucleic acid analog segmentof the unit to the probe, the detectable label, or a linker.
 10. Thecomposition according to claim 9, wherein the polymer is dextran. 11.The composition according to claim 1, wherein at least one unit furthercomprises at least one linker attaching the at least one nucleic acidanalog segment of the unit to the probe, the detectable label, or apolymer.
 12. The composition according to claim 11, wherein the linkeris chosen from a molecule comprising polyethylene glycol and a moleculecomprising at least two units according to the Formula I:

wherein R₁ and R₂ comprise NH or O, and R₃ comprises methyl, ethyl,propyl, CH₂—O—CH₂, and (CH₂—O—CH₂)₂.
 13. A method of detecting a targetin a sample comprising: contacting the composition of claim 1 with asample comprising the target such that the probe of the composition ofclaim 1 hybridizes to the target; detecting a signal for the detectablelabel of the composition of claim 1, thereby detecting the target in thesample.
 14. The method of claim 13, further comprising comparing thesignal from the target in the sample with the signal from a referencetarget or reference sample.
 15. The method of claim 13, wherein morethan one detection unit is associated with each recognition unit of thecomposition of claim
 1. 16. The method of claim 13, wherein at least twotargets are detected in the sample.
 17. The method of claim 13, whereineach unit of the composition of claim 1 comprises at least two nucleicacid analog segments.
 18. The composition according to claim 1, whereinthe at least one detection unit further comprises at least one linkerattaching the at least one nucleic acid analog segment of the unit to apolymer.
 19. The composition according to claim 1, wherein the at leastone detection unit further comprises at least one linker attaching apolymer to the detectable label.
 20. The composition according to claim1, wherein the at least one recognition unit further comprises at leastone linker attaching the at least one nucleic acid analog segment of theunit to a probe.